Starting phenix.real_space_refine on Sat Aug 8 04:45:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wdu_37465/08_2026/8wdu_37465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wdu_37465/08_2026/8wdu_37465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wdu_37465/08_2026/8wdu_37465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wdu_37465/08_2026/8wdu_37465.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wdu_37465/08_2026/8wdu_37465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wdu_37465/08_2026/8wdu_37465.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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 6 9.91 5 Fe 5 7.16 5 P 21 5.49 5 Mg 37 5.21 5 S 96 5.16 5 C 18084 2.51 5 N 3529 2.21 5 O 4496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26274 Number of models: 1 Model: "" Number of chains: 98 Chain: "C" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2429 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 283} Chain: "L" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2210 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "M" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2533 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "H" Number of atoms: 1993 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 1991 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 259, 1991 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2041 Chain: "A" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 397 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain: "E" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "F" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 397 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 335 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "I" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 324 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Q" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 331 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "S" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Chain: "T" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "U" Number of atoms: 407 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Conformer: "B" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} bond proxies already assigned to first conformer: 408 Chain: "V" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 335 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "W" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Chain: "X" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "Y" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 470 Classifications: {'peptide': 59} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 54} Chain breaks: 1 Chain: "Z" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "1" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "3" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 498 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "4" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "5" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 355 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "7" Number of atoms: 359 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 39} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 39} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 354 Chain: "8" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "9" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 251 Unusual residues: {' MG': 1, 'HEM': 4, 'PGV': 1, 'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PLM:plan-1': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 552 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 1, 'PGV': 3, 'UQ8': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 89 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: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 515 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 2, 'CRT': 1, 'LMT': 2, 'MQ8': 1, 'PGV': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-4': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'CDL': 1, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 125 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 43 Chain: "E" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'BCL': 1, 'LDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'BCL': 1, 'LDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {' CA': 1, 'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "T" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "6" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "M" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Y" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "3" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "9" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.29, per 1000 atoms: 0.20 Number of scatterers: 26274 At special positions: 0 Unit cell: (132.714, 121.806, 135.138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 5 26.01 Ca 6 19.99 S 96 16.00 P 21 15.00 Mg 37 11.99 O 4496 8.00 N 3529 7.00 C 18084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=50, symmetry=0 Number of additional bonds: simple=50, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4774 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 9 sheets defined 67.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.514A pdb=" N VAL C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 102 Processing helix chain 'C' and resid 106 through 110 Processing helix chain 'C' and resid 121 through 141 removed outlier: 3.538A pdb=" N VAL C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.959A pdb=" N CYS C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.813A pdb=" N ASP C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 244 removed outlier: 3.559A pdb=" N ALA C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.177A pdb=" N PHE C 256 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 283 removed outlier: 3.860A pdb=" N THR C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'C' and resid 323 through 331 Proline residue: C 328 - end of helix Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 32 through 57 Processing helix chain 'L' and resid 76 through 80 Processing helix chain 'L' and resid 85 through 88 Processing helix chain 'L' and resid 89 through 118 Processing helix chain 'L' and resid 121 through 139 removed outlier: 3.590A pdb=" N PHE L 129 " --> pdb=" O PHE L 125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA L 130 " --> pdb=" O ALA L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 146 Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 157 through 169 Processing helix chain 'L' and resid 170 through 171 No H-bonds generated for 'chain 'L' and resid 170 through 171' Processing helix chain 'L' and resid 172 through 175 Processing helix chain 'L' and resid 176 through 205 Processing helix chain 'L' and resid 214 through 227 removed outlier: 3.667A pdb=" N PHE L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 256 Processing helix chain 'L' and resid 264 through 269 removed outlier: 3.711A pdb=" N TRP L 268 " --> pdb=" O GLY L 264 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TRP L 269 " --> pdb=" O TRP L 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 264 through 269' Processing helix chain 'L' and resid 269 through 274 Processing helix chain 'M' and resid 37 through 44 removed outlier: 3.722A pdb=" N ILE M 43 " --> pdb=" O TRP M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 140 Processing helix chain 'M' and resid 144 through 162 Processing helix chain 'M' and resid 162 through 168 Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 179 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 227 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 263 through 287 removed outlier: 3.801A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'M' and resid 315 through 319 removed outlier: 3.664A pdb=" N THR M 319 " --> pdb=" O PRO M 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 35 Processing helix chain 'H' and resid 43 through 49 Processing helix chain 'H' and resid 70 through 73 Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 216 through 222 removed outlier: 3.513A pdb=" N ALA H 220 " --> pdb=" O ALA H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 250 removed outlier: 3.638A pdb=" N GLY H 246 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS H 247 " --> pdb=" O TYR H 243 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU H 248 " --> pdb=" O ALA H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.508A pdb=" N TRP A 9 " --> pdb=" O HIS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.737A pdb=" N LEU D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 38 Processing helix chain 'E' and resid 11 through 44 removed outlier: 3.526A pdb=" N LYS E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 11 removed outlier: 3.761A pdb=" N LEU F 11 " --> pdb=" O ILE F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 39 Processing helix chain 'G' and resid 11 through 44 Processing helix chain 'I' and resid 5 through 11 removed outlier: 4.184A pdb=" N TRP I 9 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN I 10 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 39 Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'K' and resid 13 through 39 Processing helix chain 'N' and resid 11 through 44 removed outlier: 4.004A pdb=" N GLU N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 11 removed outlier: 3.541A pdb=" N TRP O 9 " --> pdb=" O HIS O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 39 Processing helix chain 'P' and resid 11 through 44 Processing helix chain 'Q' and resid 6 through 10 removed outlier: 3.903A pdb=" N TRP Q 9 " --> pdb=" O HIS Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 39 Processing helix chain 'R' and resid 11 through 44 Processing helix chain 'S' and resid 6 through 11 removed outlier: 3.877A pdb=" N TRP S 9 " --> pdb=" O TRP S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 38 Processing helix chain 'T' and resid 11 through 44 Processing helix chain 'U' and resid 4 through 11 removed outlier: 3.544A pdb=" N LYS U 7 " --> pdb=" O ASP U 4 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE U 8 " --> pdb=" O LEU U 5 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP U 9 " --> pdb=" O TRP U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 39 Processing helix chain 'V' and resid 13 through 44 removed outlier: 3.555A pdb=" N HIS V 19 " --> pdb=" O ALA V 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 11 removed outlier: 3.937A pdb=" N LYS W 7 " --> pdb=" O ASP W 4 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP W 9 " --> pdb=" O TRP W 6 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU W 10 " --> pdb=" O LYS W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 38 Processing helix chain 'X' and resid 11 through 44 removed outlier: 3.521A pdb=" N GLY X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE X 21 " --> pdb=" O GLU X 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 11 removed outlier: 3.803A pdb=" N LYS Y 7 " --> pdb=" O ASP Y 4 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP Y 9 " --> pdb=" O TRP Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 38 Processing helix chain 'Z' and resid 11 through 44 removed outlier: 3.564A pdb=" N GLU Z 17 " --> pdb=" O GLU Z 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY Z 20 " --> pdb=" O LYS Z 16 " (cutoff:3.500A) Processing helix chain '1' and resid 7 through 12 Processing helix chain '1' and resid 13 through 39 Processing helix chain '2' and resid 11 through 44 removed outlier: 3.600A pdb=" N GLU 2 17 " --> pdb=" O GLN 2 13 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL 2 23 " --> pdb=" O HIS 2 19 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN 2 24 " --> pdb=" O GLY 2 20 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 12 Processing helix chain '3' and resid 13 through 39 Processing helix chain '3' and resid 43 through 47 Processing helix chain '4' and resid 13 through 44 Processing helix chain '5' and resid 7 through 12 removed outlier: 3.777A pdb=" N ILE 5 11 " --> pdb=" O LYS 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 39 Processing helix chain '5' and resid 40 through 43 removed outlier: 3.630A pdb=" N ASN 5 43 " --> pdb=" O PRO 5 40 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 40 through 43' Processing helix chain '6' and resid 11 through 44 Processing helix chain '7' and resid 5 through 11 Processing helix chain '7' and resid 13 through 39 removed outlier: 3.967A pdb=" N VAL 7 19 " --> pdb=" O ARG 7 15 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 44 Processing helix chain '9' and resid 7 through 12 Processing helix chain '9' and resid 13 through 39 Processing helix chain '0' and resid 11 through 44 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 Processing sheet with id=AA2, first strand: chain 'L' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AA4, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA5, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'H' and resid 66 through 68 Processing sheet with id=AA7, first strand: chain 'H' and resid 89 through 91 Processing sheet with id=AA8, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.788A pdb=" N GLU H 183 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL H 170 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR H 181 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL H 172 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE H 179 " --> pdb=" O VAL H 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.518A pdb=" N VAL H 156 " --> pdb=" O ALA H 164 " (cutoff:3.500A) 1328 hydrogen bonds defined for protein. 3748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.80 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 9182 1.38 - 1.56: 17396 1.56 - 1.75: 43 1.75 - 1.93: 180 1.93 - 2.11: 156 Bond restraints: 26957 Sorted by residual: bond pdb=" CG PRO Y 59 " pdb=" CD PRO Y 59 " ideal model delta sigma weight residual 1.503 1.235 0.268 3.40e-02 8.65e+02 6.20e+01 bond pdb=" C3 UQ8 L 309 " pdb=" C4 UQ8 L 309 " ideal model delta sigma weight residual 1.339 1.491 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C2 MQ8 M 405 " pdb=" C3 MQ8 M 405 " ideal model delta sigma weight residual 1.348 1.495 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C3 UQ8 L 304 " pdb=" C4 UQ8 L 304 " ideal model delta sigma weight residual 1.339 1.485 -0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" NA BCL L 308 " pdb="MG BCL L 308 " ideal model delta sigma weight residual 2.170 1.995 0.175 2.40e-02 1.74e+03 5.33e+01 ... (remaining 26952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 35641 5.02 - 10.04: 1303 10.04 - 15.07: 98 15.07 - 20.09: 20 20.09 - 25.11: 12 Bond angle restraints: 37074 Sorted by residual: angle pdb=" N PRO Y 59 " pdb=" CD PRO Y 59 " pdb=" CG PRO Y 59 " ideal model delta sigma weight residual 103.20 84.37 18.83 1.50e+00 4.44e-01 1.58e+02 angle pdb=" CA PRO Y 59 " pdb=" CB PRO Y 59 " pdb=" CG PRO Y 59 " ideal model delta sigma weight residual 104.50 86.85 17.65 1.90e+00 2.77e-01 8.63e+01 angle pdb=" C39 CRT V 102 " pdb=" C38 CRT V 102 " pdb=" O2 CRT V 102 " ideal model delta sigma weight residual 111.76 86.65 25.11 3.00e+00 1.11e-01 7.01e+01 angle pdb=" C40 CRT M 406 " pdb=" C38 CRT M 406 " pdb=" O2 CRT M 406 " ideal model delta sigma weight residual 111.40 86.96 24.44 3.00e+00 1.11e-01 6.64e+01 angle pdb=" C3 CRT J 103 " pdb=" C1 CRT J 103 " pdb=" C4 CRT J 103 " ideal model delta sigma weight residual 108.82 84.72 24.10 3.00e+00 1.11e-01 6.46e+01 ... (remaining 37069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 14382 36.00 - 72.00: 914 72.00 - 108.00: 178 108.00 - 144.00: 58 144.00 - 180.00: 12 Dihedral angle restraints: 15544 sinusoidal: 8173 harmonic: 7371 Sorted by residual: dihedral pdb=" C1 BCL T 101 " pdb=" CGA BCL T 101 " pdb=" O2A BCL T 101 " pdb=" CBA BCL T 101 " ideal model delta sinusoidal sigma weight residual -180.00 -74.32 -105.68 1 6.00e+00 2.78e-02 3.39e+02 dihedral pdb=" C1 BCL F 502 " pdb=" C2 BCL F 502 " pdb=" C3 BCL F 502 " pdb=" C5 BCL F 502 " ideal model delta sinusoidal sigma weight residual -180.00 -0.00 -180.00 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 3 101 " pdb=" C2 BCL 3 101 " pdb=" C3 BCL 3 101 " pdb=" C5 BCL 3 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.04 -179.96 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 15541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3334 0.080 - 0.160: 354 0.160 - 0.241: 64 0.241 - 0.321: 13 0.321 - 0.401: 7 Chirality restraints: 3772 Sorted by residual: chirality pdb=" CBD BCL M 403 " pdb=" CAD BCL M 403 " pdb=" CGD BCL M 403 " pdb=" CHA BCL M 403 " both_signs ideal model delta sigma weight residual False 2.62 3.02 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CBD BCL R 101 " pdb=" CAD BCL R 101 " pdb=" CGD BCL R 101 " pdb=" CHA BCL R 101 " both_signs ideal model delta sigma weight residual False 2.62 2.26 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CBD BCL V 101 " pdb=" CAD BCL V 101 " pdb=" CGD BCL V 101 " pdb=" CHA BCL V 101 " both_signs ideal model delta sigma weight residual False 2.62 2.26 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 3769 not shown) Planarity restraints: 4374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 0 101 " 0.370 3.00e-02 1.11e+03 3.09e-01 5.30e+02 pdb=" CBA BCL 0 101 " 0.121 3.00e-02 1.11e+03 pdb=" CGA BCL 0 101 " -0.077 3.00e-02 1.11e+03 pdb=" O1A BCL 0 101 " 0.134 3.00e-02 1.11e+03 pdb=" O2A BCL 0 101 " -0.549 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL W 101 " 0.352 3.00e-02 1.11e+03 2.86e-01 4.55e+02 pdb=" CBA BCL W 101 " 0.185 3.00e-02 1.11e+03 pdb=" CGA BCL W 101 " -0.082 3.00e-02 1.11e+03 pdb=" O1A BCL W 101 " 0.038 3.00e-02 1.11e+03 pdb=" O2A BCL W 101 " -0.493 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL K 102 " -0.354 3.00e-02 1.11e+03 2.86e-01 4.54e+02 pdb=" CBA BCL K 102 " -0.194 3.00e-02 1.11e+03 pdb=" CGA BCL K 102 " 0.085 3.00e-02 1.11e+03 pdb=" O1A BCL K 102 " -0.024 3.00e-02 1.11e+03 pdb=" O2A BCL K 102 " 0.488 3.00e-02 1.11e+03 ... (remaining 4371 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 111 2.39 - 3.02: 14469 3.02 - 3.65: 42930 3.65 - 4.27: 71895 4.27 - 4.90: 112864 Nonbonded interactions: 242269 Sorted by model distance: nonbonded pdb=" OE2 GLU M 96 " pdb=" O HOH M 501 " model vdw 1.765 3.040 nonbonded pdb=" OE1 GLU M 96 " pdb=" O HOH M 502 " model vdw 1.806 3.040 nonbonded pdb=" OE1 GLN C 183 " pdb="MG MG C 405 " model vdw 2.031 2.170 nonbonded pdb=" NE2 HIS L 196 " pdb="FE FE M 401 " model vdw 2.071 2.340 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 2.073 2.260 ... (remaining 242264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 10 through 47) selection = (chain '2' and resid 10 through 47) selection = (chain '4' and resid 10 through 47) selection = (chain '6' and resid 10 through 47) selection = (chain '8' and resid 10 through 47) selection = (chain 'B' and resid 10 through 47) selection = (chain 'J' and resid 10 through 47) selection = (chain 'N' and resid 10 through 47) selection = (chain 'P' and resid 10 through 47) selection = (chain 'R' and resid 10 through 47) } ncs_group { reference = (chain '1' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain '5' and (resid 5 through 21 or resid 23 through 46)) selection = (chain '7' and (resid 5 through 21 or resid 23 through 46)) selection = (chain '9' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'A' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'I' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'K' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'O' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'Q' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) } ncs_group { reference = (chain 'D' and (resid 2 through 33 or resid 35 through 50 or resid 102 through 1 \ 03)) selection = (chain 'F' and (resid 2 through 33 or resid 35 through 50 or resid 502 through 5 \ 03)) selection = (chain 'S' and (resid 2 through 33 or resid 35 through 50 or resid 102 through 1 \ 03)) selection = (chain 'U' and (resid 2 through 33 or resid 35 through 50 or resid 101 through 1 \ 02)) selection = (chain 'W' and (resid 2 through 33 or resid 35 through 50 or resid 101 through 1 \ 02)) } ncs_group { reference = (chain 'E' and resid 8 through 47) selection = (chain 'G' and resid 8 through 47) selection = (chain 'T' and resid 8 through 47) selection = (chain 'V' and resid 8 through 47) selection = (chain 'X' and resid 8 through 47) selection = (chain 'Z' and resid 8 through 47) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.380 Find NCS groups from input model: 0.730 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:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.465 27007 Z= 1.413 Angle : 1.900 25.111 37074 Z= 0.803 Chirality : 0.057 0.401 3772 Planarity : 0.017 0.309 4374 Dihedral : 24.529 179.998 10770 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.73 % Allowed : 18.61 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.17), residues: 2494 helix: 1.98 (0.13), residues: 1511 sheet: -0.76 (0.77), residues: 41 loop : 0.51 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 15 TYR 0.020 0.002 TYR C 319 PHE 0.026 0.002 PHE V 30 TRP 0.037 0.002 TRP S 6 HIS 0.011 0.002 HIS R 19 Details of bonding type rmsd/Z covalent geometry : bond 0.01858 / 0.80 (26957) covalent geometry : angle 1.90005 / 0.80 (37074) hydrogen bonds : bond 0.18294 / 12.17 ( 1326) hydrogen bonds : angle 6.05960 / 4.35 ( 3748) Misc. bond : bond 0.27226 / 16.80 ( 50) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 0.932 Fit side-chains REVERT: H 75 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7286 (p) REVERT: F 41 GLU cc_start: 0.7606 (tp30) cc_final: 0.7252 (tp30) REVERT: I 8 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5524 (pt) REVERT: P 27 THR cc_start: 0.7498 (m) cc_final: 0.7023 (m) REVERT: X 28 MET cc_start: 0.6580 (tpt) cc_final: 0.6213 (tpt) REVERT: Y 59 PRO cc_start: 0.6371 (Cg_exo) cc_final: 0.5699 (Cg_endo) REVERT: 4 44 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7456 (ttm170) outliers start: 37 outliers final: 26 residues processed: 301 average time/residue: 0.5715 time to fit residues: 205.2801 Evaluate side-chains 284 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain M residue 312 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 4 ASP Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 235 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 ASN C 206 GLN L 219 ASN H 71 HIS H 192 ASN A 6 HIS B 4 ASN J 24 GLN ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 6 HIS 2 16 GLN ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113083 restraints weight = 34921.169| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.18 r_work: 0.2938 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.306 27007 Z= 0.147 Angle : 0.777 16.070 37074 Z= 0.305 Chirality : 0.042 0.424 3772 Planarity : 0.005 0.067 4374 Dihedral : 20.126 179.922 6259 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.29 % Allowed : 16.28 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.17), residues: 2494 helix: 2.54 (0.12), residues: 1497 sheet: -0.83 (0.78), residues: 41 loop : 0.46 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 15 TYR 0.016 0.002 TYR M 193 PHE 0.020 0.002 PHE L 41 TRP 0.016 0.001 TRP S 6 HIS 0.008 0.001 HIS R 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (26957) covalent geometry : angle 0.77708 / 0.31 (37074) hydrogen bonds : bond 0.05134 / 3.40 ( 1326) hydrogen bonds : angle 4.31244 / 3.08 ( 3748) Misc. bond : bond 0.06524 / 2.73 ( 50) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 278 time to evaluate : 0.952 Fit side-chains REVERT: L 211 GLU cc_start: 0.8020 (pt0) cc_final: 0.7699 (mt-10) REVERT: H 48 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6777 (mtp180) REVERT: H 237 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8598 (t70) REVERT: H 259 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5705 (tp) REVERT: G 21 ILE cc_start: 0.7051 (mp) cc_final: 0.6790 (mt) REVERT: I 8 ILE cc_start: 0.5985 (OUTLIER) cc_final: 0.5741 (pt) REVERT: J 27 THR cc_start: 0.7416 (m) cc_final: 0.7113 (t) REVERT: O 10 GLN cc_start: 0.6345 (OUTLIER) cc_final: 0.6092 (mt0) REVERT: P 27 THR cc_start: 0.8078 (m) cc_final: 0.7720 (m) REVERT: S 10 LEU cc_start: 0.4525 (OUTLIER) cc_final: 0.4305 (mt) REVERT: S 15 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.6204 (ttp-110) REVERT: S 17 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7466 (mp) REVERT: Y 38 SER cc_start: 0.8710 (m) cc_final: 0.8508 (p) REVERT: 1 7 LYS cc_start: 0.5877 (OUTLIER) cc_final: 0.5577 (mmtp) REVERT: 4 7 MET cc_start: 0.4051 (OUTLIER) cc_final: 0.3704 (mtt) REVERT: 6 23 VAL cc_start: 0.8108 (t) cc_final: 0.7721 (p) REVERT: 6 30 PHE cc_start: 0.7887 (m-10) cc_final: 0.7664 (m-10) outliers start: 49 outliers final: 14 residues processed: 314 average time/residue: 0.5574 time to fit residues: 209.4325 Evaluate side-chains 283 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 259 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain O residue 10 GLN Chi-restraints excluded: chain S residue 10 LEU Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 7 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 135 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 176 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 206 GLN L 150 HIS L 207 GLN L 219 ASN M 74 ASN H 71 HIS H 103 ASN ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN P 13 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108630 restraints weight = 35997.465| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.23 r_work: 0.2859 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.336 27007 Z= 0.264 Angle : 0.919 16.922 37074 Z= 0.371 Chirality : 0.048 0.407 3772 Planarity : 0.005 0.066 4374 Dihedral : 19.946 179.744 6229 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.31 % Allowed : 14.88 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.16), residues: 2494 helix: 2.07 (0.12), residues: 1502 sheet: -0.86 (0.76), residues: 41 loop : 0.18 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 7 15 TYR 0.027 0.003 TYR C 319 PHE 0.031 0.003 PHE L 41 TRP 0.017 0.002 TRP 9 9 HIS 0.009 0.002 HIS N 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.26 (26957) covalent geometry : angle 0.91907 / 0.37 (37074) hydrogen bonds : bond 0.05918 / 3.93 ( 1326) hydrogen bonds : angle 4.51749 / 3.22 ( 3748) Misc. bond : bond 0.07708 / 3.33 ( 50) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 272 time to evaluate : 0.920 Fit side-chains REVERT: L 76 ASP cc_start: 0.8887 (m-30) cc_final: 0.8623 (m-30) REVERT: L 208 LYS cc_start: 0.5873 (OUTLIER) cc_final: 0.5292 (mppt) REVERT: H 75 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7770 (p) REVERT: H 259 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5788 (tp) REVERT: D 41 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7776 (tp30) REVERT: E 16 LYS cc_start: 0.5098 (OUTLIER) cc_final: 0.4796 (mppt) REVERT: F 41 GLU cc_start: 0.8113 (tp30) cc_final: 0.7877 (tp30) REVERT: I 8 ILE cc_start: 0.5890 (OUTLIER) cc_final: 0.5646 (pt) REVERT: J 24 GLN cc_start: 0.6610 (tt0) cc_final: 0.6211 (tp40) REVERT: J 27 THR cc_start: 0.7420 (m) cc_final: 0.7133 (t) REVERT: N 26 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.6004 (mtt) REVERT: P 13 GLN cc_start: 0.4211 (OUTLIER) cc_final: 0.3938 (tm-30) REVERT: P 24 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.6358 (mp-120) REVERT: P 27 THR cc_start: 0.8058 (m) cc_final: 0.7665 (m) REVERT: Q 15 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7323 (mtp180) REVERT: S 15 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6239 (ttp-110) REVERT: S 17 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7464 (mp) REVERT: Y 59 PRO cc_start: 0.6719 (Cg_exo) cc_final: 0.6432 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5958 (OUTLIER) cc_final: 0.5699 (mmtp) REVERT: 2 25 SER cc_start: 0.7136 (t) cc_final: 0.6664 (p) REVERT: 2 27 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7368 (m) REVERT: 3 66 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.4807 (ttp-110) REVERT: 4 14 GLU cc_start: 0.4069 (OUTLIER) cc_final: 0.3547 (mm-30) REVERT: 6 30 PHE cc_start: 0.7966 (m-10) cc_final: 0.7757 (m-10) REVERT: 7 13 ASP cc_start: 0.7799 (t0) cc_final: 0.7524 (t0) outliers start: 71 outliers final: 30 residues processed: 317 average time/residue: 0.5777 time to fit residues: 217.9784 Evaluate side-chains 303 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 14 GLU Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 6 residue 10 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 161 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN R 13 GLN ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112802 restraints weight = 29908.668| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.00 r_work: 0.2936 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.319 27007 Z= 0.155 Angle : 0.745 16.760 37074 Z= 0.299 Chirality : 0.041 0.406 3772 Planarity : 0.004 0.069 4374 Dihedral : 18.701 179.905 6229 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.08 % Allowed : 15.21 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.16), residues: 2494 helix: 2.37 (0.12), residues: 1497 sheet: -0.89 (0.78), residues: 41 loop : 0.27 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 15 TYR 0.018 0.002 TYR M 193 PHE 0.024 0.002 PHE L 41 TRP 0.015 0.001 TRP 9 9 HIS 0.006 0.001 HIS 0 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (26957) covalent geometry : angle 0.74521 / 0.30 (37074) hydrogen bonds : bond 0.05005 / 3.31 ( 1326) hydrogen bonds : angle 4.24945 / 3.03 ( 3748) Misc. bond : bond 0.06753 / 2.78 ( 50) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 267 time to evaluate : 0.900 Fit side-chains REVERT: L 208 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5349 (mppt) REVERT: L 211 GLU cc_start: 0.8038 (pt0) cc_final: 0.7735 (mt-10) REVERT: H 259 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5720 (tp) REVERT: E 28 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7162 (tpp) REVERT: I 8 ILE cc_start: 0.5912 (OUTLIER) cc_final: 0.5622 (pt) REVERT: J 27 THR cc_start: 0.7431 (m) cc_final: 0.7151 (t) REVERT: P 23 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.6815 (t) REVERT: P 24 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6344 (mp-120) REVERT: P 27 THR cc_start: 0.8096 (m) cc_final: 0.7742 (m) REVERT: Q 15 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7279 (mtp180) REVERT: S 15 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.6227 (ttp-110) REVERT: S 17 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7487 (mp) REVERT: Y 38 SER cc_start: 0.8719 (m) cc_final: 0.8491 (p) REVERT: Y 59 PRO cc_start: 0.6771 (Cg_exo) cc_final: 0.6495 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5666 (mmtp) REVERT: 2 25 SER cc_start: 0.7128 (OUTLIER) cc_final: 0.6568 (p) REVERT: 2 27 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7371 (m) REVERT: 7 13 ASP cc_start: 0.7764 (t0) cc_final: 0.7530 (t0) outliers start: 66 outliers final: 28 residues processed: 314 average time/residue: 0.5666 time to fit residues: 212.0134 Evaluate side-chains 296 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 28 MET Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 244 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 47 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109685 restraints weight = 35645.067| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.28 r_work: 0.2880 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.338 27007 Z= 0.207 Angle : 0.829 16.876 37074 Z= 0.333 Chirality : 0.044 0.407 3772 Planarity : 0.005 0.067 4374 Dihedral : 19.004 179.904 6229 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.31 % Allowed : 14.88 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.16), residues: 2494 helix: 2.21 (0.12), residues: 1498 sheet: -0.94 (0.77), residues: 41 loop : 0.20 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 192 TYR 0.024 0.003 TYR C 319 PHE 0.028 0.002 PHE L 41 TRP 0.017 0.002 TRP 9 9 HIS 0.008 0.002 HIS 0 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (26957) covalent geometry : angle 0.82879 / 0.33 (37074) hydrogen bonds : bond 0.05420 / 3.59 ( 1326) hydrogen bonds : angle 4.37125 / 3.12 ( 3748) Misc. bond : bond 0.07219 / 3.11 ( 50) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 0.886 Fit side-chains REVERT: L 208 LYS cc_start: 0.5901 (OUTLIER) cc_final: 0.5299 (mppt) REVERT: H 75 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7714 (p) REVERT: H 253 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7007 (mm-30) REVERT: H 259 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5757 (tp) REVERT: F 16 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6309 (mtt90) REVERT: F 41 GLU cc_start: 0.8101 (tp30) cc_final: 0.7884 (tp30) REVERT: I 8 ILE cc_start: 0.5906 (OUTLIER) cc_final: 0.5599 (pt) REVERT: J 24 GLN cc_start: 0.6596 (tt0) cc_final: 0.6212 (tp40) REVERT: J 27 THR cc_start: 0.7431 (m) cc_final: 0.7130 (t) REVERT: P 24 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6358 (mp-120) REVERT: P 27 THR cc_start: 0.8093 (m) cc_final: 0.7728 (m) REVERT: Q 15 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7308 (mtp180) REVERT: S 15 ARG cc_start: 0.6541 (OUTLIER) cc_final: 0.6246 (ttp-110) REVERT: S 17 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7476 (mp) REVERT: Y 59 PRO cc_start: 0.6732 (Cg_exo) cc_final: 0.6457 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5982 (OUTLIER) cc_final: 0.5738 (mmtp) REVERT: 2 25 SER cc_start: 0.7229 (OUTLIER) cc_final: 0.6776 (p) REVERT: 2 27 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7423 (m) REVERT: 7 13 ASP cc_start: 0.7770 (t0) cc_final: 0.7497 (t0) outliers start: 71 outliers final: 37 residues processed: 320 average time/residue: 0.5427 time to fit residues: 207.6637 Evaluate side-chains 305 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 8 residue 10 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 212 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 190 optimal weight: 0.0870 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112470 restraints weight = 29776.721| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.03 r_work: 0.2929 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.318 27007 Z= 0.159 Angle : 0.746 16.754 37074 Z= 0.299 Chirality : 0.041 0.402 3772 Planarity : 0.004 0.070 4374 Dihedral : 18.323 179.927 6229 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.57 % Allowed : 16.18 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.16), residues: 2494 helix: 2.37 (0.12), residues: 1498 sheet: -0.94 (0.78), residues: 41 loop : 0.27 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 15 TYR 0.018 0.002 TYR M 193 PHE 0.023 0.002 PHE L 41 TRP 0.015 0.001 TRP 9 9 HIS 0.006 0.002 HIS 0 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (26957) covalent geometry : angle 0.74578 / 0.30 (37074) hydrogen bonds : bond 0.04971 / 3.29 ( 1326) hydrogen bonds : angle 4.23148 / 3.02 ( 3748) Misc. bond : bond 0.06421 / 2.73 ( 50) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 0.832 Fit side-chains REVERT: L 208 LYS cc_start: 0.5956 (OUTLIER) cc_final: 0.5371 (mppt) REVERT: M 45 ASP cc_start: 0.8247 (t0) cc_final: 0.7820 (m-30) REVERT: H 48 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6810 (mtp180) REVERT: H 253 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6904 (mm-30) REVERT: H 259 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5686 (tp) REVERT: F 16 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6294 (mtt90) REVERT: I 8 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.5625 (pt) REVERT: J 24 GLN cc_start: 0.6587 (tt0) cc_final: 0.6200 (tp40) REVERT: J 27 THR cc_start: 0.7437 (m) cc_final: 0.7141 (t) REVERT: P 23 VAL cc_start: 0.7223 (OUTLIER) cc_final: 0.6769 (t) REVERT: P 24 GLN cc_start: 0.6721 (OUTLIER) cc_final: 0.6346 (mp-120) REVERT: P 27 THR cc_start: 0.8057 (m) cc_final: 0.7712 (m) REVERT: Q 15 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7284 (mtp180) REVERT: S 15 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.6211 (ttp-110) REVERT: S 17 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7483 (mp) REVERT: Y 38 SER cc_start: 0.8720 (m) cc_final: 0.8489 (p) REVERT: Y 41 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: Y 59 PRO cc_start: 0.6762 (Cg_exo) cc_final: 0.6495 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5993 (OUTLIER) cc_final: 0.5751 (mmtp) REVERT: 2 25 SER cc_start: 0.7206 (OUTLIER) cc_final: 0.6685 (p) REVERT: 2 27 THR cc_start: 0.7714 (OUTLIER) cc_final: 0.7370 (m) REVERT: 6 30 PHE cc_start: 0.7931 (m-10) cc_final: 0.7702 (m-10) REVERT: 7 13 ASP cc_start: 0.7755 (t0) cc_final: 0.7499 (t0) outliers start: 55 outliers final: 31 residues processed: 308 average time/residue: 0.4964 time to fit residues: 182.1180 Evaluate side-chains 305 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 206 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 10 GLN 0 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.107548 restraints weight = 33529.454| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.39 r_work: 0.2835 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.340 27007 Z= 0.266 Angle : 0.915 16.775 37074 Z= 0.368 Chirality : 0.048 0.411 3772 Planarity : 0.005 0.065 4374 Dihedral : 19.410 179.866 6229 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.40 % Allowed : 15.21 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.16), residues: 2494 helix: 2.02 (0.12), residues: 1499 sheet: -1.00 (0.76), residues: 41 loop : 0.11 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 192 TYR 0.028 0.003 TYR C 319 PHE 0.032 0.003 PHE L 41 TRP 0.018 0.002 TRP 9 9 HIS 0.012 0.003 HIS R 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.26 (26957) covalent geometry : angle 0.91548 / 0.37 (37074) hydrogen bonds : bond 0.05783 / 3.83 ( 1326) hydrogen bonds : angle 4.47187 / 3.19 ( 3748) Misc. bond : bond 0.07546 / 3.29 ( 50) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 264 time to evaluate : 0.885 Fit side-chains REVERT: C 260 LYS cc_start: 0.8955 (mtpp) cc_final: 0.8478 (ttpt) REVERT: L 76 ASP cc_start: 0.8867 (m-30) cc_final: 0.8636 (m-30) REVERT: L 208 LYS cc_start: 0.5883 (OUTLIER) cc_final: 0.5285 (mppt) REVERT: M 45 ASP cc_start: 0.8347 (t0) cc_final: 0.7875 (m-30) REVERT: H 75 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7750 (p) REVERT: H 253 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6989 (mm-30) REVERT: H 259 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5754 (tp) REVERT: B 13 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6599 (tp40) REVERT: F 16 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6320 (mtt90) REVERT: I 8 ILE cc_start: 0.5872 (OUTLIER) cc_final: 0.5612 (pt) REVERT: J 24 GLN cc_start: 0.6581 (tt0) cc_final: 0.6206 (tp40) REVERT: J 27 THR cc_start: 0.7433 (m) cc_final: 0.7127 (t) REVERT: P 24 GLN cc_start: 0.6784 (OUTLIER) cc_final: 0.6368 (mp-120) REVERT: P 27 THR cc_start: 0.8060 (m) cc_final: 0.7678 (m) REVERT: Q 15 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7296 (mtp180) REVERT: S 15 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.6287 (ttp-110) REVERT: S 17 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7472 (mp) REVERT: Y 41 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: Y 59 PRO cc_start: 0.6715 (Cg_exo) cc_final: 0.6459 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.6021 (OUTLIER) cc_final: 0.5765 (mmtp) REVERT: 2 25 SER cc_start: 0.7314 (OUTLIER) cc_final: 0.6915 (p) REVERT: 3 66 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.4742 (ttp-110) REVERT: 6 30 PHE cc_start: 0.8028 (m-10) cc_final: 0.7805 (m-10) REVERT: 7 13 ASP cc_start: 0.7734 (t0) cc_final: 0.7452 (t0) outliers start: 73 outliers final: 38 residues processed: 315 average time/residue: 0.5404 time to fit residues: 201.7912 Evaluate side-chains 309 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 257 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 8 residue 10 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 194 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 109 optimal weight: 0.7980 chunk 239 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108369 restraints weight = 32251.718| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.37 r_work: 0.2854 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.331 27007 Z= 0.209 Angle : 0.834 16.590 37074 Z= 0.336 Chirality : 0.044 0.409 3772 Planarity : 0.005 0.070 4374 Dihedral : 18.975 179.923 6229 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.99 % Allowed : 15.58 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.16), residues: 2494 helix: 2.11 (0.12), residues: 1497 sheet: -0.99 (0.76), residues: 41 loop : 0.12 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 192 TYR 0.024 0.003 TYR C 319 PHE 0.029 0.002 PHE L 41 TRP 0.021 0.002 TRP S 6 HIS 0.011 0.002 HIS R 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (26957) covalent geometry : angle 0.83364 / 0.34 (37074) hydrogen bonds : bond 0.05417 / 3.59 ( 1326) hydrogen bonds : angle 4.38293 / 3.13 ( 3748) Misc. bond : bond 0.07101 / 3.07 ( 50) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 0.859 Fit side-chains REVERT: C 260 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8485 (ttpt) REVERT: C 304 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9000 (mtmp) REVERT: L 208 LYS cc_start: 0.5921 (OUTLIER) cc_final: 0.5313 (mppt) REVERT: M 45 ASP cc_start: 0.8318 (t0) cc_final: 0.7853 (m-30) REVERT: H 75 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7667 (p) REVERT: H 253 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6927 (mm-30) REVERT: H 259 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5742 (tp) REVERT: B 13 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6574 (tp40) REVERT: D 41 GLU cc_start: 0.8363 (tp30) cc_final: 0.7803 (tp30) REVERT: F 16 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6265 (mtt90) REVERT: I 8 ILE cc_start: 0.5922 (OUTLIER) cc_final: 0.5681 (pt) REVERT: I 10 GLN cc_start: 0.5009 (OUTLIER) cc_final: 0.3694 (tm-30) REVERT: J 24 GLN cc_start: 0.6593 (tt0) cc_final: 0.6217 (tp40) REVERT: J 27 THR cc_start: 0.7406 (m) cc_final: 0.7098 (t) REVERT: P 23 VAL cc_start: 0.7234 (OUTLIER) cc_final: 0.6761 (t) REVERT: P 24 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6362 (mp-120) REVERT: P 27 THR cc_start: 0.8058 (m) cc_final: 0.7709 (m) REVERT: Q 15 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7285 (mtp180) REVERT: S 15 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.6292 (ttp-110) REVERT: S 17 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7431 (mp) REVERT: Y 41 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: Y 59 PRO cc_start: 0.6702 (Cg_exo) cc_final: 0.6439 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.6016 (OUTLIER) cc_final: 0.5760 (mmtp) REVERT: 2 25 SER cc_start: 0.7263 (OUTLIER) cc_final: 0.6877 (p) REVERT: 6 30 PHE cc_start: 0.8057 (m-10) cc_final: 0.7828 (m-10) REVERT: 7 13 ASP cc_start: 0.7736 (t0) cc_final: 0.7431 (t0) REVERT: 8 26 MET cc_start: 0.8419 (ttm) cc_final: 0.8110 (ttm) outliers start: 64 outliers final: 36 residues processed: 311 average time/residue: 0.4737 time to fit residues: 175.3621 Evaluate side-chains 307 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 255 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 10 GLN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 8 residue 10 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 166 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111689 restraints weight = 35741.251| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.40 r_work: 0.2888 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.303 27007 Z= 0.146 Angle : 0.734 16.388 37074 Z= 0.295 Chirality : 0.040 0.400 3772 Planarity : 0.004 0.068 4374 Dihedral : 18.017 179.985 6229 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.33 % Allowed : 16.32 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.16), residues: 2494 helix: 2.39 (0.12), residues: 1494 sheet: -0.94 (0.78), residues: 41 loop : 0.26 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 15 TYR 0.018 0.002 TYR M 193 PHE 0.023 0.002 PHE L 41 TRP 0.029 0.001 TRP S 6 HIS 0.009 0.001 HIS R 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (26957) covalent geometry : angle 0.73450 / 0.29 (37074) hydrogen bonds : bond 0.04833 / 3.20 ( 1326) hydrogen bonds : angle 4.22111 / 3.02 ( 3748) Misc. bond : bond 0.06271 / 2.70 ( 50) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 270 time to evaluate : 0.731 Fit side-chains REVERT: L 208 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.5312 (mppt) REVERT: L 211 GLU cc_start: 0.8018 (pt0) cc_final: 0.7713 (mt-10) REVERT: M 45 ASP cc_start: 0.8298 (t0) cc_final: 0.7800 (m-30) REVERT: H 48 ARG cc_start: 0.6972 (mtp180) cc_final: 0.6692 (mtp85) REVERT: H 253 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6929 (mm-30) REVERT: H 259 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5715 (tp) REVERT: E 47 LEU cc_start: 0.7908 (mt) cc_final: 0.7707 (mt) REVERT: I 8 ILE cc_start: 0.5899 (OUTLIER) cc_final: 0.5687 (pt) REVERT: J 24 GLN cc_start: 0.6597 (tt0) cc_final: 0.6212 (tp40) REVERT: J 27 THR cc_start: 0.7409 (m) cc_final: 0.7079 (t) REVERT: P 23 VAL cc_start: 0.7203 (OUTLIER) cc_final: 0.6747 (t) REVERT: P 24 GLN cc_start: 0.6731 (OUTLIER) cc_final: 0.6364 (mp-120) REVERT: P 27 THR cc_start: 0.8054 (m) cc_final: 0.7721 (m) REVERT: S 15 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.6227 (ttp-110) REVERT: S 17 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7425 (mp) REVERT: Y 38 SER cc_start: 0.8765 (m) cc_final: 0.8515 (p) REVERT: 1 7 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5709 (mmtp) REVERT: 2 25 SER cc_start: 0.7189 (OUTLIER) cc_final: 0.6740 (p) REVERT: 2 27 THR cc_start: 0.7644 (t) cc_final: 0.7344 (m) REVERT: 3 16 MET cc_start: 0.5817 (mmt) cc_final: 0.5415 (tpt) REVERT: 6 30 PHE cc_start: 0.8019 (m-10) cc_final: 0.7784 (m-10) REVERT: 7 13 ASP cc_start: 0.7722 (t0) cc_final: 0.7480 (t0) REVERT: 8 26 MET cc_start: 0.8360 (ttm) cc_final: 0.8031 (ttm) outliers start: 50 outliers final: 33 residues processed: 309 average time/residue: 0.5275 time to fit residues: 194.8133 Evaluate side-chains 299 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 157 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 chunk 238 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111955 restraints weight = 26690.701| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.04 r_work: 0.2891 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.327 27007 Z= 0.186 Angle : 0.796 16.440 37074 Z= 0.321 Chirality : 0.042 0.402 3772 Planarity : 0.005 0.068 4374 Dihedral : 18.337 179.964 6229 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.05 % Allowed : 16.88 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.16), residues: 2494 helix: 2.28 (0.12), residues: 1496 sheet: -0.99 (0.78), residues: 41 loop : 0.18 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 44 TYR 0.022 0.002 TYR C 319 PHE 0.027 0.002 PHE L 41 TRP 0.039 0.002 TRP S 6 HIS 0.010 0.002 HIS R 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (26957) covalent geometry : angle 0.79592 / 0.32 (37074) hydrogen bonds : bond 0.05209 / 3.45 ( 1326) hydrogen bonds : angle 4.31443 / 3.08 ( 3748) Misc. bond : bond 0.07086 / 3.11 ( 50) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 0.917 Fit side-chains REVERT: L 208 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.5323 (mppt) REVERT: M 45 ASP cc_start: 0.8294 (t0) cc_final: 0.7842 (m-30) REVERT: H 48 ARG cc_start: 0.6965 (mtp180) cc_final: 0.6735 (mtp180) REVERT: H 253 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6903 (mm-30) REVERT: H 259 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5738 (tp) REVERT: J 24 GLN cc_start: 0.6569 (tt0) cc_final: 0.6187 (tp40) REVERT: J 27 THR cc_start: 0.7415 (m) cc_final: 0.7097 (t) REVERT: P 24 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.6311 (mp-120) REVERT: P 27 THR cc_start: 0.8059 (m) cc_final: 0.7717 (m) REVERT: S 15 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.6256 (ttp-110) REVERT: S 17 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7478 (mp) REVERT: 1 7 LYS cc_start: 0.6028 (OUTLIER) cc_final: 0.5761 (mmtp) REVERT: 2 25 SER cc_start: 0.7261 (OUTLIER) cc_final: 0.6866 (p) REVERT: 2 27 THR cc_start: 0.7674 (t) cc_final: 0.7349 (m) REVERT: 6 30 PHE cc_start: 0.8012 (m-10) cc_final: 0.7778 (m-10) REVERT: 7 13 ASP cc_start: 0.7760 (t0) cc_final: 0.7485 (t0) REVERT: 8 26 MET cc_start: 0.8362 (ttm) cc_final: 0.8048 (ttm) outliers start: 44 outliers final: 36 residues processed: 295 average time/residue: 0.5802 time to fit residues: 203.5644 Evaluate side-chains 295 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 4 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 181 optimal weight: 0.0770 chunk 175 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.148918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109557 restraints weight = 33780.059| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.40 r_work: 0.2864 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.324 27007 Z= 0.180 Angle : 0.788 16.330 37074 Z= 0.318 Chirality : 0.042 0.404 3772 Planarity : 0.005 0.068 4374 Dihedral : 18.248 179.992 6227 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.19 % Allowed : 16.88 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.16), residues: 2494 helix: 2.26 (0.12), residues: 1497 sheet: -1.01 (0.77), residues: 41 loop : 0.18 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 44 TYR 0.021 0.002 TYR C 319 PHE 0.026 0.002 PHE L 41 TRP 0.036 0.002 TRP S 6 HIS 0.010 0.002 HIS R 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (26957) covalent geometry : angle 0.78814 / 0.32 (37074) hydrogen bonds : bond 0.05163 / 3.42 ( 1326) hydrogen bonds : angle 4.31499 / 3.08 ( 3748) Misc. bond : bond 0.07000 / 3.05 ( 50) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12059.53 seconds wall clock time: 205 minutes 49.64 seconds (12349.64 seconds total)