Starting phenix.real_space_refine on Sun Jul 5 03:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f0l_31400/07_2026/7f0l_31400.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f0l_31400/07_2026/7f0l_31400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f0l_31400/07_2026/7f0l_31400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f0l_31400/07_2026/7f0l_31400.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f0l_31400/07_2026/7f0l_31400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f0l_31400/07_2026/7f0l_31400.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7f0l_31400/07_2026/7f0l_31400.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f0l_31400/07_2026/7f0l_31400.cif" } resolution = 2.94 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= 0.016 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 21 5.49 5 Mg 32 5.21 5 S 88 5.16 5 C 16545 2.51 5 N 3101 2.21 5 O 3670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23458 Number of models: 1 Model: "" Number of chains: 66 Chain: "L" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "H" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1864 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} 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} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "G" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "I" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 454 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "V" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "W" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "1" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "4" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "5" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "6" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 332 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "7" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "8" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "X" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 405 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "U" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 369 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "L" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 482 Unusual residues: {'BCL': 3, 'BPH': 1, 'LDA': 2, 'PGV': 3, 'U10': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 49 Chain: "M" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 497 Unusual residues: {' FE': 1, 'BCL': 1, 'BPH': 1, 'CDL': 1, 'LDA': 1, 'LMT': 3, 'PGV': 2, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 284 Unusual residues: {'CDL': 2, 'LMT': 2, 'PGV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 158 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 193 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 184 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'BCL': 1, 'LMT': 2, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 205 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 169 Unusual residues: {'BCL': 1, 'CDL': 1, 'LDA': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "5" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 183 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "6" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 141 Unusual residues: {'LDA': 2, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 4.79, per 1000 atoms: 0.20 Number of scatterers: 23458 At special positions: 0 Unit cell: (132.374, 114.87, 137.844, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 88 16.00 P 21 15.00 Mg 32 11.99 O 3670 8.00 N 3101 7.00 C 16545 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 897.5 milliseconds 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 8 sheets defined 72.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'L' and resid 6 through 10 removed outlier: 3.610A pdb=" N ARG L 10 " --> pdb=" O ARG L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.575A pdb=" N VAL L 54 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 74 removed outlier: 3.589A pdb=" N GLY L 74 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 112 removed outlier: 3.523A pdb=" N GLU L 106 " --> pdb=" O LEU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.628A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.810A pdb=" N TYR L 144 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 164 removed outlier: 3.640A pdb=" N ASP L 155 " --> pdb=" O TRP L 151 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 169 removed outlier: 5.929A pdb=" N HIS L 168 " --> pdb=" O GLY L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 removed outlier: 3.549A pdb=" N PHE L 216 " --> pdb=" O GLU L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 250 removed outlier: 3.899A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 262 No H-bonds generated for 'chain 'L' and resid 260 through 262' Processing helix chain 'L' and resid 263 through 268 removed outlier: 3.670A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 41 Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 112 through 140 removed outlier: 3.731A pdb=" N LEU M 116 " --> pdb=" O GLY M 112 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA M 137 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.612A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU M 156 " --> pdb=" O SER M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 180 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 removed outlier: 3.623A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.861A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 282 " --> pdb=" O LEU M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 300 Processing helix chain 'H' and resid 12 through 34 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.510A pdb=" N LEU H 212 " --> pdb=" O SER H 209 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 239 Processing helix chain 'H' and resid 239 through 244 Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 12 through 38 removed outlier: 4.280A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 45 removed outlier: 3.584A pdb=" N GLN B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 10 removed outlier: 3.747A pdb=" N LYS D 6 " --> pdb=" O LYS D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 38 removed outlier: 3.565A pdb=" N VAL D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 42 through 51 removed outlier: 3.514A pdb=" N SER D 47 " --> pdb=" O TRP D 43 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 45 Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.658A pdb=" N LYS F 6 " --> pdb=" O LYS F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 39 through 41 No H-bonds generated for 'chain 'F' and resid 39 through 41' Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'G' and resid 12 through 45 Processing helix chain 'I' and resid 1 through 10 removed outlier: 3.967A pdb=" N TYR I 5 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 38 Processing helix chain 'I' and resid 42 through 52 Processing helix chain 'J' and resid 12 through 45 Processing helix chain 'K' and resid 3 through 10 removed outlier: 3.864A pdb=" N LYS K 6 " --> pdb=" O LYS K 3 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP K 8 " --> pdb=" O TYR K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 37 removed outlier: 3.584A pdb=" N VAL K 18 " --> pdb=" O ARG K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'N' and resid 12 through 45 Processing helix chain 'O' and resid 3 through 10 removed outlier: 3.685A pdb=" N TRP O 8 " --> pdb=" O TYR O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 38 Processing helix chain 'O' and resid 42 through 52 removed outlier: 3.633A pdb=" N SER O 47 " --> pdb=" O TRP O 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 52 removed outlier: 3.509A pdb=" N ALA Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 45 removed outlier: 3.602A pdb=" N VAL R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 10 Processing helix chain 'S' and resid 12 through 38 removed outlier: 3.837A pdb=" N VAL S 18 " --> pdb=" O ARG S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 12 through 45 Processing helix chain 'V' and resid 2 through 10 removed outlier: 4.048A pdb=" N TYR V 5 " --> pdb=" O SER V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 38 Processing helix chain 'V' and resid 42 through 52 Processing helix chain 'W' and resid 12 through 45 removed outlier: 3.502A pdb=" N VAL W 22 " --> pdb=" O GLU W 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 8 removed outlier: 3.802A pdb=" N TRP Y 8 " --> pdb=" O TYR Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 38 Processing helix chain 'Y' and resid 42 through 52 Processing helix chain 'Z' and resid 12 through 45 Processing helix chain '1' and resid 3 through 10 removed outlier: 3.605A pdb=" N LYS 1 6 " --> pdb=" O LYS 1 3 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 38 Processing helix chain '1' and resid 42 through 51 removed outlier: 3.543A pdb=" N ALA 1 48 " --> pdb=" O LEU 1 44 " (cutoff:3.500A) Processing helix chain '2' and resid 12 through 45 Processing helix chain '3' and resid 3 through 5 No H-bonds generated for 'chain '3' and resid 3 through 5' Processing helix chain '3' and resid 6 through 11 Processing helix chain '3' and resid 12 through 38 Processing helix chain '3' and resid 42 through 52 Processing helix chain '4' and resid 12 through 45 Processing helix chain '5' and resid 3 through 10 removed outlier: 3.729A pdb=" N LYS 5 6 " --> pdb=" O LYS 5 3 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE 5 10 " --> pdb=" O ILE 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 38 Processing helix chain '5' and resid 42 through 51 Processing helix chain '6' and resid 12 through 45 Processing helix chain '7' and resid 6 through 11 Processing helix chain '7' and resid 12 through 38 removed outlier: 3.550A pdb=" N PHE 7 17 " --> pdb=" O PRO 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 51 Processing helix chain '8' and resid 12 through 45 Processing helix chain 'X' and resid 18 through 54 Processing helix chain 'U' and resid 5 through 30 Processing helix chain 'U' and resid 31 through 48 removed outlier: 3.709A pdb=" N GLY U 35 " --> pdb=" O HIS U 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.806A pdb=" N PHE L 24 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.829A pdb=" N GLN M 11 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 93 through 94 Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.002A pdb=" N PHE H 7 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 62 through 65 Processing sheet with id=AA6, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA7, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.822A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL H 169 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA H 176 " --> pdb=" O VAL H 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.357A pdb=" N VAL H 153 " --> pdb=" O ALA H 161 " (cutoff:3.500A) 1271 hydrogen bonds defined for protein. 3600 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: 3.64 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 6887 1.37 - 1.54: 17020 1.54 - 1.71: 113 1.71 - 1.88: 171 1.88 - 2.05: 128 Bond restraints: 24319 Sorted by residual: bond pdb=" CB7 CDL Y 102 " pdb=" OB8 CDL Y 102 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL H 304 " pdb=" OA8 CDL H 304 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL H 305 " pdb=" OA8 CDL H 305 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL H 304 " pdb=" OB8 CDL H 304 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 bond pdb=" CA7 CDL Y 102 " pdb=" OA8 CDL Y 102 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.16e+02 ... (remaining 24314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 30783 3.72 - 7.45: 2092 7.45 - 11.17: 296 11.17 - 14.90: 55 14.90 - 18.62: 13 Bond angle restraints: 33239 Sorted by residual: angle pdb=" C51 CDL M 811 " pdb=" CB5 CDL M 811 " pdb=" OB6 CDL M 811 " ideal model delta sigma weight residual 111.33 122.29 -10.96 1.32e+00 5.72e-01 6.87e+01 angle pdb=" C1D BCL L 301 " pdb=" C2D BCL L 301 " pdb=" CMD BCL L 301 " ideal model delta sigma weight residual 125.57 139.28 -13.71 1.83e+00 2.99e-01 5.63e+01 angle pdb=" C1D BCL 8 102 " pdb=" C2D BCL 8 102 " pdb=" CMD BCL 8 102 " ideal model delta sigma weight residual 125.57 139.06 -13.49 1.83e+00 2.99e-01 5.44e+01 angle pdb=" C1D BCL M 803 " pdb=" C2D BCL M 803 " pdb=" CMD BCL M 803 " ideal model delta sigma weight residual 125.57 139.05 -13.48 1.83e+00 2.99e-01 5.44e+01 angle pdb=" C1D BCL A 703 " pdb=" C2D BCL A 703 " pdb=" CMD BCL A 703 " ideal model delta sigma weight residual 125.57 138.97 -13.40 1.83e+00 2.99e-01 5.37e+01 ... (remaining 33234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 12101 35.96 - 71.92: 486 71.92 - 107.89: 28 107.89 - 143.85: 6 143.85 - 179.81: 7 Dihedral angle restraints: 12628 sinusoidal: 6046 harmonic: 6582 Sorted by residual: dihedral pdb=" C1 BCL L 309 " pdb=" C2 BCL L 309 " pdb=" C3 BCL L 309 " pdb=" C5 BCL L 309 " ideal model delta sinusoidal sigma weight residual -180.00 -0.66 -179.34 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" CBD BCL L 301 " pdb=" CGD BCL L 301 " pdb=" O2D BCL L 301 " pdb=" CED BCL L 301 " ideal model delta sinusoidal sigma weight residual 180.00 135.34 44.66 1 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CBD BCL M 803 " pdb=" CGD BCL M 803 " pdb=" O2D BCL M 803 " pdb=" CED BCL M 803 " ideal model delta sinusoidal sigma weight residual 180.00 137.91 42.09 1 5.00e+00 4.00e-02 9.90e+01 ... (remaining 12625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2645 0.057 - 0.115: 511 0.115 - 0.172: 123 0.172 - 0.230: 41 0.230 - 0.287: 15 Chirality restraints: 3335 Sorted by residual: chirality pdb=" C05 PGV Q 103 " pdb=" C04 PGV Q 103 " pdb=" C06 PGV Q 103 " pdb=" O05 PGV Q 103 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C05 PGV L 305 " pdb=" C04 PGV L 305 " pdb=" C06 PGV L 305 " pdb=" O05 PGV L 305 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C05 PGV X 101 " pdb=" C04 PGV X 101 " pdb=" C06 PGV X 101 " pdb=" O05 PGV X 101 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3332 not shown) Planarity restraints: 3930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A BCL 8 102 " -0.080 3.20e-02 9.77e+02 2.46e-01 2.95e+02 pdb=" C4A BCL 8 102 " -0.035 3.20e-02 9.77e+02 pdb=" CHA BCL 8 102 " 0.264 3.20e-02 9.77e+02 pdb=" CHB BCL 8 102 " 0.252 3.20e-02 9.77e+02 pdb=" NA BCL 8 102 " -0.402 3.20e-02 9.77e+02 delta sigma weight rms_deltas residual plane pdb=" C1 BPH M 804 " 0.178 2.00e-02 2.50e+03 1.47e-01 2.70e+02 pdb=" C2 BPH M 804 " -0.223 2.00e-02 2.50e+03 pdb=" C3 BPH M 804 " -0.077 2.00e-02 2.50e+03 pdb=" C4 BPH M 804 " -0.020 2.00e-02 2.50e+03 pdb=" C5 BPH M 804 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL W 101 " -0.271 3.00e-02 1.11e+03 2.17e-01 2.61e+02 pdb=" CBA BCL W 101 " -0.178 3.00e-02 1.11e+03 pdb=" CGA BCL W 101 " 0.069 3.00e-02 1.11e+03 pdb=" O1A BCL W 101 " 0.027 3.00e-02 1.11e+03 pdb=" O2A BCL W 101 " 0.353 3.00e-02 1.11e+03 ... (remaining 3927 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 148 2.57 - 3.15: 17150 3.15 - 3.74: 36713 3.74 - 4.32: 56462 4.32 - 4.90: 91637 Nonbonded interactions: 202110 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 805 " model vdw 1.988 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 805 " model vdw 2.084 2.260 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 805 " model vdw 2.167 2.340 nonbonded pdb=" O1B LMT H 301 " pdb=" O6' LMT H 301 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR D 41 " pdb=" O ARG E 45 " model vdw 2.191 3.040 ... (remaining 202105 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 '1' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain '3' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain '5' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain '7' and (resid 4 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'D' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 54)) selection = (chain 'F' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'I' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'K' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'O' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'Q' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'S' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'V' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'Y' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) } ncs_group { reference = (chain '2' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '4' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '6' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '8' and resid 11 through 48) selection = (chain 'B' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'E' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'J' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'N' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'P' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'R' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'T' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'W' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'Z' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) } 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=1.00 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.640 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.020 0.542 24351 Z= 1.171 Angle : 1.896 18.619 33239 Z= 0.803 Chirality : 0.056 0.287 3335 Planarity : 0.016 0.246 3930 Dihedral : 17.832 179.811 8398 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.93 % Allowed : 4.72 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.03 (0.17), residues: 2199 helix: 0.29 (0.12), residues: 1500 sheet: -0.43 (1.15), residues: 24 loop : -0.30 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 53 TYR 0.011 0.002 TYR R 8 PHE 0.011 0.001 PHE H 10 TRP 0.012 0.002 TRP M 252 HIS 0.008 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.01885 / 0.85 (24319) covalent geometry : angle 1.89554 / 0.80 (33239) hydrogen bonds : bond 0.22690 / 15.15 ( 1269) hydrogen bonds : angle 6.74408 / 4.86 ( 3600) Misc. bond : bond 0.22272 / 15.15 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 350 time to evaluate : 0.753 Fit side-chains REVERT: L 102 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8799 (mt) REVERT: L 248 MET cc_start: 0.8663 (mmm) cc_final: 0.8450 (mmm) REVERT: M 263 GLU cc_start: 0.8522 (tt0) cc_final: 0.8095 (tt0) REVERT: M 292 ASP cc_start: 0.7462 (p0) cc_final: 0.7245 (p0) REVERT: H 30 TYR cc_start: 0.8642 (t80) cc_final: 0.8438 (t80) REVERT: H 52 ASN cc_start: 0.8675 (p0) cc_final: 0.8258 (p0) REVERT: H 128 HIS cc_start: 0.7854 (m-70) cc_final: 0.7498 (m170) REVERT: H 182 GLU cc_start: 0.7962 (tt0) cc_final: 0.7620 (tt0) REVERT: A 6 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8279 (mtmt) REVERT: B 11 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 17 GLN cc_start: 0.8325 (mt0) cc_final: 0.7954 (mt0) REVERT: G 14 GLU cc_start: 0.7372 (pm20) cc_final: 0.7151 (pm20) REVERT: I 5 TYR cc_start: 0.8568 (p90) cc_final: 0.8353 (p90) REVERT: K 12 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7666 (t0) REVERT: O 15 ARG cc_start: 0.7071 (tmm160) cc_final: 0.6440 (mtp85) REVERT: O 45 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7099 (mm-30) REVERT: P 25 SER cc_start: 0.8657 (t) cc_final: 0.8374 (p) REVERT: P 29 LEU cc_start: 0.8610 (tp) cc_final: 0.7944 (tp) REVERT: Q 5 TYR cc_start: 0.8225 (p90) cc_final: 0.7913 (p90) REVERT: Q 6 LYS cc_start: 0.8043 (mttm) cc_final: 0.7751 (mttt) REVERT: V 6 LYS cc_start: 0.7624 (mmmm) cc_final: 0.7070 (mmmt) REVERT: V 45 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7594 (mm-30) REVERT: Z 15 GLN cc_start: 0.7782 (mt0) cc_final: 0.7455 (mt0) REVERT: Z 45 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7906 (ttt-90) REVERT: 2 18 GLU cc_start: 0.7005 (tp30) cc_final: 0.6530 (tp30) REVERT: 3 5 TYR cc_start: 0.7517 (p90) cc_final: 0.7273 (p90) REVERT: 3 27 LEU cc_start: 0.8707 (tp) cc_final: 0.8470 (tp) REVERT: 5 18 VAL cc_start: 0.8043 (t) cc_final: 0.7841 (t) REVERT: 5 30 MET cc_start: 0.8055 (ttp) cc_final: 0.7844 (ttp) REVERT: 6 13 ASP cc_start: 0.6134 (t0) cc_final: 0.5275 (t0) REVERT: 6 15 GLN cc_start: 0.5722 (mt0) cc_final: 0.5114 (mm110) REVERT: 7 30 MET cc_start: 0.7313 (mmt) cc_final: 0.7023 (mmt) REVERT: 7 51 TYR cc_start: 0.7620 (m-80) cc_final: 0.7362 (m-80) REVERT: U 24 MET cc_start: 0.7676 (ptp) cc_final: 0.7325 (ptp) outliers start: 36 outliers final: 19 residues processed: 378 average time/residue: 0.5628 time to fit residues: 247.9484 Evaluate side-chains 320 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 297 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 272 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain X residue 17 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 301 HIS G 17 GLN K 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 17 GLN V 20 GLN 5 52 ASN X 66 ASN U 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.100551 restraints weight = 27812.877| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.25 r_work: 0.2814 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24351 Z= 0.142 Angle : 0.697 14.710 33239 Z= 0.276 Chirality : 0.038 0.304 3335 Planarity : 0.004 0.054 3930 Dihedral : 18.014 179.317 4526 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.95 % Allowed : 10.61 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.92 (0.18), residues: 2199 helix: 1.94 (0.13), residues: 1523 sheet: 0.37 (0.95), residues: 34 loop : -0.25 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 247 TYR 0.011 0.001 TYR R 8 PHE 0.012 0.001 PHE M 201 TRP 0.012 0.001 TRP M 252 HIS 0.006 0.001 HIS I 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (24319) covalent geometry : angle 0.69739 / 0.28 (33239) hydrogen bonds : bond 0.05766 / 3.92 ( 1269) hydrogen bonds : angle 3.82128 / 2.74 ( 3600) Misc. bond : bond 0.00248 / 0.15 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 311 time to evaluate : 0.827 Fit side-chains REVERT: L 102 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8765 (mt) REVERT: L 248 MET cc_start: 0.8848 (mmm) cc_final: 0.8584 (mmm) REVERT: M 86 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8713 (tp) REVERT: M 210 TYR cc_start: 0.8783 (m-10) cc_final: 0.8532 (m-10) REVERT: M 216 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8867 (t80) REVERT: H 30 TYR cc_start: 0.8702 (t80) cc_final: 0.8373 (t80) REVERT: H 52 ASN cc_start: 0.8741 (p0) cc_final: 0.8225 (p0) REVERT: H 128 HIS cc_start: 0.7672 (m-70) cc_final: 0.7358 (m170) REVERT: H 175 MET cc_start: 0.8775 (ptm) cc_final: 0.8464 (ptp) REVERT: H 182 GLU cc_start: 0.8627 (tt0) cc_final: 0.8037 (tt0) REVERT: B 11 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8265 (mp) REVERT: B 17 GLN cc_start: 0.8271 (mt0) cc_final: 0.7909 (mt0) REVERT: B 24 MET cc_start: 0.8531 (tpp) cc_final: 0.8221 (mmt) REVERT: G 6 LEU cc_start: 0.3322 (OUTLIER) cc_final: 0.2821 (mt) REVERT: G 43 ILE cc_start: 0.8669 (mt) cc_final: 0.8415 (mm) REVERT: K 6 LYS cc_start: 0.8574 (mmtp) cc_final: 0.8368 (mmtp) REVERT: K 12 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7540 (t0) REVERT: N 24 MET cc_start: 0.8673 (mmp) cc_final: 0.8159 (mmt) REVERT: P 25 SER cc_start: 0.8688 (t) cc_final: 0.8239 (p) REVERT: P 29 LEU cc_start: 0.8362 (tp) cc_final: 0.7726 (tp) REVERT: Q 3 LYS cc_start: 0.8073 (mttp) cc_final: 0.7345 (mttp) REVERT: S 3 LYS cc_start: 0.8342 (ttmm) cc_final: 0.7878 (mtpp) REVERT: T 8 TYR cc_start: 0.7240 (m-80) cc_final: 0.6929 (m-80) REVERT: V 45 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8197 (mm-30) REVERT: W 24 MET cc_start: 0.8082 (mmm) cc_final: 0.7786 (mmm) REVERT: Z 15 GLN cc_start: 0.7542 (mt0) cc_final: 0.7134 (mt0) REVERT: 3 5 TYR cc_start: 0.7298 (p90) cc_final: 0.6999 (p90) REVERT: 5 53 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7545 (mtm180) REVERT: 6 11 LEU cc_start: 0.6456 (mm) cc_final: 0.6109 (mp) REVERT: 6 13 ASP cc_start: 0.6236 (t0) cc_final: 0.5734 (t70) REVERT: 6 15 GLN cc_start: 0.5646 (mt0) cc_final: 0.5086 (mm110) REVERT: 7 51 TYR cc_start: 0.7448 (m-80) cc_final: 0.7028 (m-80) REVERT: 8 39 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7684 (tp) REVERT: X 26 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7737 (mm-40) REVERT: X 29 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7834 (ttmt) REVERT: X 53 ARG cc_start: 0.7292 (mtm110) cc_final: 0.6602 (mtt90) REVERT: X 59 GLU cc_start: 0.6241 (mp0) cc_final: 0.5816 (mp0) REVERT: U 24 MET cc_start: 0.7566 (ptp) cc_final: 0.7300 (ptp) outliers start: 55 outliers final: 20 residues processed: 342 average time/residue: 0.5506 time to fit residues: 221.0841 Evaluate side-chains 315 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 286 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain 2 residue 11 LEU Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 5 residue 7 ILE Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 66 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 167 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 28 ASN H 44 ASN F 20 GLN O 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 60 ASN X 66 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.123642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.098245 restraints weight = 28039.293| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.15 r_work: 0.2782 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24351 Z= 0.246 Angle : 0.813 18.234 33239 Z= 0.319 Chirality : 0.042 0.292 3335 Planarity : 0.004 0.056 3930 Dihedral : 18.299 179.812 4510 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.59 % Allowed : 12.11 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.76 (0.17), residues: 2199 helix: 1.89 (0.12), residues: 1518 sheet: 0.32 (0.92), residues: 34 loop : -0.49 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 14 TYR 0.013 0.002 TYR 5 5 PHE 0.016 0.002 PHE H 20 TRP 0.015 0.002 TRP M 252 HIS 0.008 0.002 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.25 (24319) covalent geometry : angle 0.81323 / 0.32 (33239) hydrogen bonds : bond 0.05702 / 3.86 ( 1269) hydrogen bonds : angle 3.80660 / 2.73 ( 3600) Misc. bond : bond 0.00355 / 0.22 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 300 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: L 102 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8800 (mt) REVERT: L 248 MET cc_start: 0.8922 (mmm) cc_final: 0.8673 (mmm) REVERT: M 210 TYR cc_start: 0.8771 (m-10) cc_final: 0.8516 (m-10) REVERT: M 216 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8978 (t80) REVERT: H 30 TYR cc_start: 0.8708 (t80) cc_final: 0.8380 (t80) REVERT: H 128 HIS cc_start: 0.7721 (m-70) cc_final: 0.7475 (m170) REVERT: H 182 GLU cc_start: 0.8602 (tt0) cc_final: 0.7989 (tt0) REVERT: B 11 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8271 (mp) REVERT: B 17 GLN cc_start: 0.8360 (mt0) cc_final: 0.7971 (mt0) REVERT: B 24 MET cc_start: 0.8639 (tpp) cc_final: 0.8243 (mmt) REVERT: G 43 ILE cc_start: 0.8654 (mt) cc_final: 0.8375 (mm) REVERT: J 35 ILE cc_start: 0.8668 (mt) cc_final: 0.8458 (mt) REVERT: O 6 LYS cc_start: 0.8337 (mtmp) cc_final: 0.7520 (mttm) REVERT: P 25 SER cc_start: 0.8740 (t) cc_final: 0.8233 (p) REVERT: P 29 LEU cc_start: 0.8414 (tp) cc_final: 0.7800 (tp) REVERT: Q 3 LYS cc_start: 0.8100 (mttp) cc_final: 0.7347 (mttt) REVERT: Q 5 TYR cc_start: 0.8384 (p90) cc_final: 0.8034 (p90) REVERT: Q 20 GLN cc_start: 0.7662 (mt0) cc_final: 0.7434 (mm-40) REVERT: R 18 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6972 (tp30) REVERT: S 3 LYS cc_start: 0.8371 (ttmm) cc_final: 0.8029 (mtpp) REVERT: S 37 SER cc_start: 0.8610 (m) cc_final: 0.8409 (m) REVERT: V 45 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8132 (mm-30) REVERT: W 24 MET cc_start: 0.8132 (mmm) cc_final: 0.7853 (mmt) REVERT: Y 36 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8855 (mt) REVERT: Z 15 GLN cc_start: 0.7720 (mt0) cc_final: 0.7379 (mt0) REVERT: 3 5 TYR cc_start: 0.7229 (p90) cc_final: 0.6902 (p90) REVERT: 5 30 MET cc_start: 0.8076 (ttp) cc_final: 0.7802 (ttp) REVERT: 5 51 TYR cc_start: 0.8021 (m-80) cc_final: 0.7106 (m-80) REVERT: 5 53 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.5243 (mpp-170) REVERT: 6 13 ASP cc_start: 0.5991 (t0) cc_final: 0.5291 (t70) REVERT: 6 15 GLN cc_start: 0.5967 (mt0) cc_final: 0.5329 (mm110) REVERT: 7 24 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7188 (mp) REVERT: 7 51 TYR cc_start: 0.7457 (m-80) cc_final: 0.7060 (m-80) REVERT: 8 30 PHE cc_start: 0.6597 (t80) cc_final: 0.6385 (t80) REVERT: X 53 ARG cc_start: 0.7346 (mtm110) cc_final: 0.6592 (mtt90) REVERT: X 59 GLU cc_start: 0.6461 (mp0) cc_final: 0.6046 (mp0) REVERT: U 24 MET cc_start: 0.7690 (ptp) cc_final: 0.7298 (ptp) outliers start: 67 outliers final: 38 residues processed: 341 average time/residue: 0.5160 time to fit residues: 207.1825 Evaluate side-chains 326 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 272 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 15 ARG Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 36 LEU Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 2 residue 11 LEU Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 2 residue 33 VAL Chi-restraints excluded: chain 3 residue 29 VAL Chi-restraints excluded: chain 5 residue 7 ILE Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 24 LEU Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 68 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 184 optimal weight: 0.1980 chunk 131 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 20 GLN O 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.126965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.101271 restraints weight = 27855.591| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.23 r_work: 0.2827 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24351 Z= 0.126 Angle : 0.648 17.771 33239 Z= 0.252 Chirality : 0.037 0.270 3335 Planarity : 0.003 0.053 3930 Dihedral : 17.057 179.750 4507 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.00 % Allowed : 14.04 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.33 (0.18), residues: 2199 helix: 2.38 (0.12), residues: 1518 sheet: 0.48 (0.95), residues: 34 loop : -0.46 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 45 TYR 0.011 0.001 TYR M 76 PHE 0.011 0.001 PHE H 20 TRP 0.013 0.001 TRP M 252 HIS 0.005 0.001 HIS L 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (24319) covalent geometry : angle 0.64783 / 0.25 (33239) hydrogen bonds : bond 0.04564 / 3.09 ( 1269) hydrogen bonds : angle 3.48017 / 2.49 ( 3600) Misc. bond : bond 0.00203 / 0.13 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: L 102 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8663 (mt) REVERT: L 248 MET cc_start: 0.8861 (mmm) cc_final: 0.8585 (mmm) REVERT: M 20 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8226 (mtp) REVERT: M 86 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8666 (tp) REVERT: M 210 TYR cc_start: 0.8756 (m-10) cc_final: 0.8511 (m-10) REVERT: M 236 GLU cc_start: 0.7730 (tp30) cc_final: 0.7492 (tp30) REVERT: H 30 TYR cc_start: 0.8674 (t80) cc_final: 0.8364 (t80) REVERT: H 52 ASN cc_start: 0.8845 (p0) cc_final: 0.8425 (p0) REVERT: H 122 GLU cc_start: 0.7407 (tt0) cc_final: 0.7151 (tt0) REVERT: H 128 HIS cc_start: 0.7691 (m-70) cc_final: 0.7407 (m170) REVERT: H 182 GLU cc_start: 0.8645 (tt0) cc_final: 0.8028 (tt0) REVERT: A 6 LYS cc_start: 0.8488 (mttp) cc_final: 0.8017 (mttt) REVERT: B 17 GLN cc_start: 0.8047 (mt0) cc_final: 0.7664 (mt0) REVERT: B 24 MET cc_start: 0.8576 (tpp) cc_final: 0.8171 (mmt) REVERT: G 6 LEU cc_start: 0.3292 (OUTLIER) cc_final: 0.2789 (mt) REVERT: G 43 ILE cc_start: 0.8566 (mt) cc_final: 0.8330 (mm) REVERT: K 6 LYS cc_start: 0.8560 (mmtp) cc_final: 0.8339 (mmtp) REVERT: O 6 LYS cc_start: 0.8275 (mtmp) cc_final: 0.7657 (mttm) REVERT: P 25 SER cc_start: 0.8685 (t) cc_final: 0.8283 (p) REVERT: P 29 LEU cc_start: 0.8342 (tp) cc_final: 0.7684 (tp) REVERT: Q 5 TYR cc_start: 0.8234 (p90) cc_final: 0.7863 (p90) REVERT: Q 20 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7207 (mm-40) REVERT: R 18 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6942 (tp30) REVERT: S 3 LYS cc_start: 0.8336 (ttmm) cc_final: 0.7950 (mtpp) REVERT: T 35 ILE cc_start: 0.8682 (mt) cc_final: 0.8442 (mm) REVERT: V 45 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8188 (mm-30) REVERT: W 24 MET cc_start: 0.8081 (mmm) cc_final: 0.7810 (mmm) REVERT: Z 15 GLN cc_start: 0.7754 (mt0) cc_final: 0.7306 (mt0) REVERT: 2 29 LEU cc_start: 0.8481 (tp) cc_final: 0.8232 (tt) REVERT: 3 5 TYR cc_start: 0.7281 (p90) cc_final: 0.6974 (p90) REVERT: 5 30 MET cc_start: 0.8052 (ttp) cc_final: 0.7782 (ttp) REVERT: 5 53 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7547 (ttm170) REVERT: 6 15 GLN cc_start: 0.5959 (mt0) cc_final: 0.5316 (mm110) REVERT: 7 51 TYR cc_start: 0.7385 (m-80) cc_final: 0.6992 (m-80) REVERT: 8 39 LEU cc_start: 0.7871 (tt) cc_final: 0.7627 (tp) REVERT: X 53 ARG cc_start: 0.7300 (mtm110) cc_final: 0.6571 (mtt90) REVERT: X 54 MET cc_start: 0.7858 (ptm) cc_final: 0.7468 (ptt) REVERT: X 59 GLU cc_start: 0.6415 (mp0) cc_final: 0.5959 (mp0) REVERT: U 24 MET cc_start: 0.7667 (ptp) cc_final: 0.7355 (ptp) outliers start: 56 outliers final: 23 residues processed: 346 average time/residue: 0.5031 time to fit residues: 205.5193 Evaluate side-chains 316 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 286 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 7 ILE Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 66 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 177 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.101403 restraints weight = 27713.033| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.22 r_work: 0.2826 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24351 Z= 0.130 Angle : 0.649 17.698 33239 Z= 0.252 Chirality : 0.037 0.271 3335 Planarity : 0.003 0.054 3930 Dihedral : 16.622 179.712 4501 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.16 % Allowed : 14.95 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.48 (0.18), residues: 2199 helix: 2.51 (0.12), residues: 1518 sheet: 0.56 (0.96), residues: 34 loop : -0.43 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 45 TYR 0.011 0.001 TYR L 73 PHE 0.013 0.001 PHE 8 30 TRP 0.012 0.001 TRP M 252 HIS 0.005 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (24319) covalent geometry : angle 0.64916 / 0.25 (33239) hydrogen bonds : bond 0.04505 / 3.05 ( 1269) hydrogen bonds : angle 3.42541 / 2.45 ( 3600) Misc. bond : bond 0.00211 / 0.13 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 302 time to evaluate : 0.982 Fit side-chains REVERT: L 102 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8737 (mt) REVERT: L 248 MET cc_start: 0.8889 (mmm) cc_final: 0.8575 (mmm) REVERT: M 20 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8245 (mtp) REVERT: M 60 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8230 (mm) REVERT: M 86 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8672 (tp) REVERT: M 210 TYR cc_start: 0.8743 (m-10) cc_final: 0.8513 (m-10) REVERT: M 216 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8788 (t80) REVERT: M 236 GLU cc_start: 0.7740 (tp30) cc_final: 0.7519 (tp30) REVERT: H 30 TYR cc_start: 0.8681 (t80) cc_final: 0.8333 (t80) REVERT: H 43 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6502 (mm-30) REVERT: H 45 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7627 (mm-30) REVERT: H 52 ASN cc_start: 0.8851 (p0) cc_final: 0.8454 (p0) REVERT: H 128 HIS cc_start: 0.7729 (m-70) cc_final: 0.7494 (m170) REVERT: H 130 LYS cc_start: 0.8135 (tttm) cc_final: 0.7872 (tttt) REVERT: H 182 GLU cc_start: 0.8655 (tt0) cc_final: 0.8045 (tt0) REVERT: B 17 GLN cc_start: 0.8131 (mt0) cc_final: 0.7751 (mt0) REVERT: B 24 MET cc_start: 0.8619 (tpp) cc_final: 0.8210 (mmt) REVERT: G 6 LEU cc_start: 0.3330 (OUTLIER) cc_final: 0.2925 (pp) REVERT: G 43 ILE cc_start: 0.8540 (mt) cc_final: 0.8310 (mm) REVERT: O 6 LYS cc_start: 0.8241 (mtmp) cc_final: 0.7620 (mttm) REVERT: O 11 PHE cc_start: 0.7571 (m-80) cc_final: 0.7252 (m-80) REVERT: P 25 SER cc_start: 0.8700 (t) cc_final: 0.8311 (p) REVERT: P 29 LEU cc_start: 0.8387 (tp) cc_final: 0.7730 (tp) REVERT: Q 5 TYR cc_start: 0.8247 (p90) cc_final: 0.7835 (p90) REVERT: Q 20 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7228 (mm-40) REVERT: R 18 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6923 (tp30) REVERT: S 3 LYS cc_start: 0.8392 (ttmm) cc_final: 0.7952 (mtpp) REVERT: T 35 ILE cc_start: 0.8718 (mt) cc_final: 0.8462 (mm) REVERT: V 45 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8171 (mm-30) REVERT: W 24 MET cc_start: 0.8106 (mmm) cc_final: 0.7760 (mmm) REVERT: Z 15 GLN cc_start: 0.7769 (mt0) cc_final: 0.7322 (mt0) REVERT: 2 29 LEU cc_start: 0.8514 (tp) cc_final: 0.8298 (tt) REVERT: 3 5 TYR cc_start: 0.7313 (p90) cc_final: 0.7000 (p90) REVERT: 5 30 MET cc_start: 0.8073 (ttp) cc_final: 0.7781 (ttp) REVERT: 5 53 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7605 (ttm170) REVERT: 6 15 GLN cc_start: 0.5997 (mt0) cc_final: 0.5390 (mm110) REVERT: 7 51 TYR cc_start: 0.7390 (m-80) cc_final: 0.7016 (m-80) REVERT: 8 30 PHE cc_start: 0.6411 (t80) cc_final: 0.6080 (t80) REVERT: 8 39 LEU cc_start: 0.7983 (tt) cc_final: 0.7780 (tp) REVERT: X 53 ARG cc_start: 0.7432 (mtm110) cc_final: 0.6676 (mtt90) REVERT: X 54 MET cc_start: 0.7869 (ptm) cc_final: 0.7506 (ptt) REVERT: X 59 GLU cc_start: 0.6438 (mp0) cc_final: 0.6053 (mp0) REVERT: U 24 MET cc_start: 0.7680 (ptp) cc_final: 0.7367 (ptp) REVERT: U 27 PHE cc_start: 0.7843 (t80) cc_final: 0.7512 (t80) outliers start: 59 outliers final: 29 residues processed: 339 average time/residue: 0.4876 time to fit residues: 195.9585 Evaluate side-chains 321 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 52 ASN Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 152 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100332 restraints weight = 27849.638| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.22 r_work: 0.2811 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24351 Z= 0.155 Angle : 0.684 17.510 33239 Z= 0.267 Chirality : 0.038 0.259 3335 Planarity : 0.003 0.055 3930 Dihedral : 16.761 179.738 4499 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.48 % Allowed : 15.01 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.38 (0.17), residues: 2199 helix: 2.45 (0.12), residues: 1517 sheet: 0.58 (0.96), residues: 34 loop : -0.52 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 6 45 TYR 0.011 0.001 TYR L 73 PHE 0.014 0.001 PHE H 20 TRP 0.013 0.001 TRP M 252 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (24319) covalent geometry : angle 0.68408 / 0.27 (33239) hydrogen bonds : bond 0.04707 / 3.19 ( 1269) hydrogen bonds : angle 3.46271 / 2.47 ( 3600) Misc. bond : bond 0.00253 / 0.16 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 300 time to evaluate : 0.886 Fit side-chains REVERT: L 102 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8711 (mt) REVERT: L 248 MET cc_start: 0.8912 (mmm) cc_final: 0.8614 (mmm) REVERT: M 20 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8232 (mtp) REVERT: M 60 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8269 (mm) REVERT: M 86 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8690 (tp) REVERT: M 210 TYR cc_start: 0.8755 (m-10) cc_final: 0.8540 (m-10) REVERT: H 30 TYR cc_start: 0.8675 (t80) cc_final: 0.8337 (t80) REVERT: H 43 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6656 (mm-30) REVERT: H 45 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7638 (mm-30) REVERT: H 52 ASN cc_start: 0.8855 (p0) cc_final: 0.8469 (p0) REVERT: H 122 GLU cc_start: 0.7376 (tt0) cc_final: 0.7048 (tt0) REVERT: H 128 HIS cc_start: 0.7690 (m-70) cc_final: 0.7471 (m170) REVERT: H 182 GLU cc_start: 0.8655 (tt0) cc_final: 0.8041 (tt0) REVERT: B 17 GLN cc_start: 0.8158 (mt0) cc_final: 0.7754 (mt0) REVERT: B 24 MET cc_start: 0.8631 (tpp) cc_final: 0.8231 (mmt) REVERT: G 6 LEU cc_start: 0.3310 (OUTLIER) cc_final: 0.2800 (mt) REVERT: G 43 ILE cc_start: 0.8568 (mt) cc_final: 0.8343 (mm) REVERT: O 6 LYS cc_start: 0.8294 (mtmp) cc_final: 0.7588 (mttm) REVERT: O 11 PHE cc_start: 0.7572 (m-80) cc_final: 0.7318 (m-80) REVERT: P 25 SER cc_start: 0.8707 (t) cc_final: 0.8310 (p) REVERT: P 29 LEU cc_start: 0.8355 (tp) cc_final: 0.7712 (tp) REVERT: Q 5 TYR cc_start: 0.8281 (p90) cc_final: 0.7870 (p90) REVERT: Q 20 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7316 (mm-40) REVERT: R 18 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6969 (tp30) REVERT: S 3 LYS cc_start: 0.8464 (ttmm) cc_final: 0.7989 (mtpp) REVERT: T 35 ILE cc_start: 0.8659 (mt) cc_final: 0.8430 (mm) REVERT: V 20 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: V 45 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8121 (mm-30) REVERT: W 24 MET cc_start: 0.8049 (mmm) cc_final: 0.7813 (mmm) REVERT: Z 15 GLN cc_start: 0.7789 (mt0) cc_final: 0.7353 (mt0) REVERT: 2 29 LEU cc_start: 0.8517 (tp) cc_final: 0.8295 (tt) REVERT: 3 5 TYR cc_start: 0.7273 (p90) cc_final: 0.6983 (p90) REVERT: 5 15 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.4554 (tmt170) REVERT: 5 30 MET cc_start: 0.8091 (ttp) cc_final: 0.7793 (ttp) REVERT: 5 53 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7584 (ttm170) REVERT: 6 13 ASP cc_start: 0.5831 (t0) cc_final: 0.5040 (t70) REVERT: 6 15 GLN cc_start: 0.6000 (mt0) cc_final: 0.5391 (mm110) REVERT: 7 51 TYR cc_start: 0.7403 (m-80) cc_final: 0.7031 (m-80) REVERT: 8 30 PHE cc_start: 0.6406 (t80) cc_final: 0.6081 (t80) REVERT: X 53 ARG cc_start: 0.7450 (mtm110) cc_final: 0.6670 (mtt90) REVERT: X 59 GLU cc_start: 0.6441 (mp0) cc_final: 0.6095 (mp0) REVERT: U 24 MET cc_start: 0.7688 (ptp) cc_final: 0.7338 (ptp) REVERT: U 27 PHE cc_start: 0.7864 (t80) cc_final: 0.7640 (t80) outliers start: 65 outliers final: 32 residues processed: 337 average time/residue: 0.5114 time to fit residues: 203.1072 Evaluate side-chains 326 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 283 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 230 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 15 ARG Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 52 ASN Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 8 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.101887 restraints weight = 27755.507| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.22 r_work: 0.2838 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24351 Z= 0.124 Angle : 0.636 17.023 33239 Z= 0.248 Chirality : 0.037 0.260 3335 Planarity : 0.003 0.053 3930 Dihedral : 16.380 179.743 4499 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.89 % Allowed : 16.02 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.56 (0.18), residues: 2199 helix: 2.59 (0.12), residues: 1519 sheet: 0.68 (0.97), residues: 34 loop : -0.49 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 45 TYR 0.011 0.001 TYR I 5 PHE 0.012 0.001 PHE H 20 TRP 0.012 0.001 TRP M 252 HIS 0.005 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (24319) covalent geometry : angle 0.63578 / 0.25 (33239) hydrogen bonds : bond 0.04399 / 2.98 ( 1269) hydrogen bonds : angle 3.37034 / 2.41 ( 3600) Misc. bond : bond 0.00193 / 0.12 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 293 time to evaluate : 0.839 Fit side-chains REVERT: L 102 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8689 (mt) REVERT: L 248 MET cc_start: 0.8907 (mmm) cc_final: 0.8575 (mmm) REVERT: M 20 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8210 (mtp) REVERT: M 60 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8221 (mm) REVERT: M 86 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8678 (tp) REVERT: M 210 TYR cc_start: 0.8736 (m-10) cc_final: 0.8481 (m-10) REVERT: M 216 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8773 (t80) REVERT: H 30 TYR cc_start: 0.8680 (t80) cc_final: 0.8360 (t80) REVERT: H 43 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6590 (mm-30) REVERT: H 52 ASN cc_start: 0.8807 (p0) cc_final: 0.8460 (p0) REVERT: H 122 GLU cc_start: 0.7396 (tt0) cc_final: 0.7024 (tt0) REVERT: H 128 HIS cc_start: 0.7705 (m-70) cc_final: 0.7430 (m170) REVERT: H 130 LYS cc_start: 0.8092 (tttm) cc_final: 0.7652 (ttmm) REVERT: H 182 GLU cc_start: 0.8617 (tt0) cc_final: 0.7987 (tt0) REVERT: B 17 GLN cc_start: 0.8142 (mt0) cc_final: 0.7771 (mt0) REVERT: B 24 MET cc_start: 0.8610 (tpp) cc_final: 0.8218 (mmt) REVERT: G 6 LEU cc_start: 0.3316 (OUTLIER) cc_final: 0.2919 (pp) REVERT: G 43 ILE cc_start: 0.8530 (mt) cc_final: 0.8324 (mm) REVERT: O 6 LYS cc_start: 0.8255 (mtmp) cc_final: 0.7607 (mttm) REVERT: O 11 PHE cc_start: 0.7494 (m-80) cc_final: 0.7221 (m-80) REVERT: P 25 SER cc_start: 0.8675 (t) cc_final: 0.8318 (p) REVERT: P 29 LEU cc_start: 0.8369 (tp) cc_final: 0.7738 (tp) REVERT: Q 5 TYR cc_start: 0.8288 (p90) cc_final: 0.7892 (p90) REVERT: Q 20 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7197 (mm-40) REVERT: R 18 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: S 3 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8038 (mtpp) REVERT: T 35 ILE cc_start: 0.8661 (mt) cc_final: 0.8446 (mm) REVERT: V 20 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: V 45 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8132 (mm-30) REVERT: W 24 MET cc_start: 0.8123 (mmm) cc_final: 0.7797 (mmm) REVERT: Z 15 GLN cc_start: 0.7748 (mt0) cc_final: 0.7277 (mt0) REVERT: 2 29 LEU cc_start: 0.8459 (tp) cc_final: 0.8247 (tt) REVERT: 3 5 TYR cc_start: 0.7273 (p90) cc_final: 0.7026 (p90) REVERT: 5 15 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.4510 (tmt170) REVERT: 5 30 MET cc_start: 0.8124 (ttp) cc_final: 0.7867 (ttp) REVERT: 5 53 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7650 (ttm170) REVERT: 6 13 ASP cc_start: 0.5910 (t0) cc_final: 0.5182 (t70) REVERT: 7 51 TYR cc_start: 0.7391 (m-80) cc_final: 0.7027 (m-80) REVERT: 8 30 PHE cc_start: 0.6405 (t80) cc_final: 0.6048 (t80) REVERT: 8 39 LEU cc_start: 0.7723 (tp) cc_final: 0.7425 (tt) REVERT: X 53 ARG cc_start: 0.7396 (mtm110) cc_final: 0.6653 (mtt90) REVERT: X 54 MET cc_start: 0.7878 (ptm) cc_final: 0.7494 (ptt) REVERT: X 59 GLU cc_start: 0.6388 (mp0) cc_final: 0.6045 (mp0) REVERT: U 24 MET cc_start: 0.7661 (ptp) cc_final: 0.7327 (ptp) REVERT: U 27 PHE cc_start: 0.7841 (t80) cc_final: 0.7593 (t80) outliers start: 54 outliers final: 27 residues processed: 325 average time/residue: 0.4738 time to fit residues: 182.0467 Evaluate side-chains 319 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 280 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 3 residue 10 ILE Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 15 ARG Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 204 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098695 restraints weight = 27923.198| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.21 r_work: 0.2786 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24351 Z= 0.223 Angle : 0.776 17.752 33239 Z= 0.302 Chirality : 0.041 0.262 3335 Planarity : 0.004 0.057 3930 Dihedral : 17.207 179.792 4498 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.95 % Allowed : 16.24 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.17), residues: 2199 helix: 2.26 (0.12), residues: 1517 sheet: 0.50 (0.94), residues: 34 loop : -0.60 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 233 TYR 0.014 0.002 TYR I 5 PHE 0.018 0.002 PHE H 20 TRP 0.013 0.002 TRP M 157 HIS 0.007 0.002 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.22 (24319) covalent geometry : angle 0.77621 / 0.30 (33239) hydrogen bonds : bond 0.05170 / 3.50 ( 1269) hydrogen bonds : angle 3.57567 / 2.55 ( 3600) Misc. bond : bond 0.00326 / 0.20 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 284 time to evaluate : 0.759 Fit side-chains REVERT: L 102 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8767 (mt) REVERT: L 248 MET cc_start: 0.8943 (mmm) cc_final: 0.8709 (mmm) REVERT: M 13 ARG cc_start: 0.7316 (ttm170) cc_final: 0.7043 (ttm170) REVERT: M 20 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8255 (mtp) REVERT: M 60 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8320 (mm) REVERT: M 86 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8678 (tp) REVERT: M 210 TYR cc_start: 0.8762 (m-10) cc_final: 0.8538 (m-10) REVERT: M 216 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8906 (t80) REVERT: H 30 TYR cc_start: 0.8705 (t80) cc_final: 0.8386 (t80) REVERT: H 43 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6666 (mm-30) REVERT: H 52 ASN cc_start: 0.8878 (p0) cc_final: 0.8476 (p0) REVERT: H 122 GLU cc_start: 0.7409 (tt0) cc_final: 0.7100 (tt0) REVERT: H 182 GLU cc_start: 0.8660 (tt0) cc_final: 0.8037 (tt0) REVERT: B 17 GLN cc_start: 0.8176 (mt0) cc_final: 0.7765 (mt0) REVERT: B 24 MET cc_start: 0.8646 (tpp) cc_final: 0.8241 (mmt) REVERT: F 15 ARG cc_start: 0.8330 (mtp85) cc_final: 0.8082 (mtp-110) REVERT: G 6 LEU cc_start: 0.3348 (OUTLIER) cc_final: 0.2836 (mt) REVERT: G 43 ILE cc_start: 0.8597 (mt) cc_final: 0.8352 (mm) REVERT: N 24 MET cc_start: 0.8656 (mmt) cc_final: 0.8201 (mmt) REVERT: O 6 LYS cc_start: 0.8379 (mtmp) cc_final: 0.7685 (mttm) REVERT: P 25 SER cc_start: 0.8696 (t) cc_final: 0.8278 (p) REVERT: P 29 LEU cc_start: 0.8412 (tp) cc_final: 0.7831 (tp) REVERT: Q 3 LYS cc_start: 0.8104 (mttp) cc_final: 0.7347 (mttt) REVERT: Q 5 TYR cc_start: 0.8327 (p90) cc_final: 0.7902 (p90) REVERT: Q 20 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7345 (mm-40) REVERT: R 18 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6921 (tp30) REVERT: S 3 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8066 (mtpp) REVERT: T 35 ILE cc_start: 0.8664 (mt) cc_final: 0.8440 (mm) REVERT: V 45 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8065 (mm-30) REVERT: W 24 MET cc_start: 0.8108 (mmm) cc_final: 0.7842 (mmm) REVERT: Z 15 GLN cc_start: 0.7880 (mt0) cc_final: 0.7450 (mt0) REVERT: 2 29 LEU cc_start: 0.8549 (tp) cc_final: 0.8317 (tt) REVERT: 3 5 TYR cc_start: 0.7331 (p90) cc_final: 0.7090 (p90) REVERT: 5 15 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.4606 (tmt170) REVERT: 5 30 MET cc_start: 0.8113 (ttp) cc_final: 0.7824 (ttp) REVERT: 5 53 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7603 (mtt180) REVERT: 6 13 ASP cc_start: 0.6204 (t0) cc_final: 0.5390 (t70) REVERT: 6 15 GLN cc_start: 0.6020 (mt0) cc_final: 0.5400 (mm110) REVERT: 7 51 TYR cc_start: 0.7499 (m-80) cc_final: 0.7092 (m-80) REVERT: X 59 GLU cc_start: 0.6514 (mp0) cc_final: 0.6274 (mp0) REVERT: U 24 MET cc_start: 0.7698 (ptp) cc_final: 0.7327 (ptp) REVERT: U 27 PHE cc_start: 0.7848 (t80) cc_final: 0.7627 (t80) outliers start: 55 outliers final: 34 residues processed: 319 average time/residue: 0.5105 time to fit residues: 190.5370 Evaluate side-chains 318 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 9 MET Chi-restraints excluded: chain 5 residue 15 ARG Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 52 ASN Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 142 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.127317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.101915 restraints weight = 27875.076| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.21 r_work: 0.2832 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24351 Z= 0.123 Angle : 0.649 16.755 33239 Z= 0.253 Chirality : 0.037 0.254 3335 Planarity : 0.003 0.054 3930 Dihedral : 16.514 179.756 4498 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.57 % Allowed : 16.83 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.46 (0.18), residues: 2199 helix: 2.53 (0.12), residues: 1519 sheet: 0.62 (0.97), residues: 34 loop : -0.55 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 233 TYR 0.013 0.001 TYR I 5 PHE 0.012 0.001 PHE H 20 TRP 0.013 0.001 TRP P 28 HIS 0.005 0.001 HIS M 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (24319) covalent geometry : angle 0.64919 / 0.25 (33239) hydrogen bonds : bond 0.04452 / 3.02 ( 1269) hydrogen bonds : angle 3.40584 / 2.43 ( 3600) Misc. bond : bond 0.00184 / 0.11 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 0.809 Fit side-chains REVERT: L 102 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8662 (mt) REVERT: L 248 MET cc_start: 0.8893 (mmm) cc_final: 0.8589 (mmm) REVERT: M 20 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8184 (mtp) REVERT: M 60 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8226 (mm) REVERT: M 86 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8665 (tp) REVERT: M 210 TYR cc_start: 0.8743 (m-10) cc_final: 0.8495 (m-10) REVERT: M 236 GLU cc_start: 0.7644 (tp30) cc_final: 0.7389 (tp30) REVERT: H 30 TYR cc_start: 0.8684 (t80) cc_final: 0.8384 (t80) REVERT: H 43 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6650 (mm-30) REVERT: H 52 ASN cc_start: 0.8855 (p0) cc_final: 0.8454 (p0) REVERT: H 122 GLU cc_start: 0.7400 (tt0) cc_final: 0.7148 (tt0) REVERT: H 182 GLU cc_start: 0.8636 (tt0) cc_final: 0.8003 (tt0) REVERT: B 17 GLN cc_start: 0.8139 (mt0) cc_final: 0.7768 (mt0) REVERT: B 24 MET cc_start: 0.8599 (tpp) cc_final: 0.8201 (mmt) REVERT: F 15 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7923 (mtp-110) REVERT: G 6 LEU cc_start: 0.3316 (OUTLIER) cc_final: 0.2920 (pp) REVERT: G 43 ILE cc_start: 0.8544 (mt) cc_final: 0.8320 (mm) REVERT: O 6 LYS cc_start: 0.8282 (mtmp) cc_final: 0.7651 (mttm) REVERT: P 25 SER cc_start: 0.8645 (t) cc_final: 0.8308 (p) REVERT: P 29 LEU cc_start: 0.8384 (tp) cc_final: 0.7759 (tp) REVERT: Q 5 TYR cc_start: 0.8304 (p90) cc_final: 0.7895 (p90) REVERT: Q 20 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7199 (mm-40) REVERT: R 18 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6905 (tp30) REVERT: S 3 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8056 (mtpp) REVERT: T 35 ILE cc_start: 0.8564 (mt) cc_final: 0.8347 (mm) REVERT: V 20 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: V 45 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8135 (mm-30) REVERT: W 24 MET cc_start: 0.8088 (mmm) cc_final: 0.7836 (mmm) REVERT: Z 15 GLN cc_start: 0.7843 (mt0) cc_final: 0.7447 (mt0) REVERT: 2 29 LEU cc_start: 0.8493 (tp) cc_final: 0.8248 (tt) REVERT: 3 5 TYR cc_start: 0.7245 (p90) cc_final: 0.7007 (p90) REVERT: 5 15 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.4531 (tmt170) REVERT: 5 30 MET cc_start: 0.8166 (ttp) cc_final: 0.7910 (ttp) REVERT: 5 53 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7595 (ttm170) REVERT: 6 13 ASP cc_start: 0.6021 (t0) cc_final: 0.5278 (t70) REVERT: 7 51 TYR cc_start: 0.7455 (m-80) cc_final: 0.7105 (m-80) REVERT: 8 30 PHE cc_start: 0.6506 (t80) cc_final: 0.6130 (t80) REVERT: 8 39 LEU cc_start: 0.7630 (tp) cc_final: 0.7331 (tt) REVERT: X 53 ARG cc_start: 0.7344 (mtm110) cc_final: 0.6663 (mtt90) REVERT: X 59 GLU cc_start: 0.6493 (mp0) cc_final: 0.6234 (mp0) REVERT: U 24 MET cc_start: 0.7660 (ptp) cc_final: 0.7448 (ptp) REVERT: U 27 PHE cc_start: 0.7779 (t80) cc_final: 0.7540 (t80) outliers start: 48 outliers final: 28 residues processed: 316 average time/residue: 0.5222 time to fit residues: 193.8494 Evaluate side-chains 316 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 3 residue 10 ILE Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 15 ARG Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 52 ASN Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.9990 chunk 101 optimal weight: 0.0980 chunk 160 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 199 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.127854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.102415 restraints weight = 27883.600| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.21 r_work: 0.2850 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24351 Z= 0.118 Angle : 0.633 16.660 33239 Z= 0.250 Chirality : 0.036 0.254 3335 Planarity : 0.003 0.054 3930 Dihedral : 16.107 179.708 4498 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.20 % Allowed : 17.42 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.61 (0.18), residues: 2199 helix: 2.64 (0.12), residues: 1519 sheet: 0.80 (0.99), residues: 34 loop : -0.51 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 45 TYR 0.014 0.001 TYR I 5 PHE 0.014 0.001 PHE M 216 TRP 0.019 0.001 TRP P 28 HIS 0.005 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (24319) covalent geometry : angle 0.63278 / 0.25 (33239) hydrogen bonds : bond 0.04316 / 2.92 ( 1269) hydrogen bonds : angle 3.34345 / 2.39 ( 3600) Misc. bond : bond 0.00177 / 0.11 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: L 248 MET cc_start: 0.8894 (mmm) cc_final: 0.8541 (mmm) REVERT: M 60 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8361 (mm) REVERT: M 86 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8658 (tp) REVERT: M 210 TYR cc_start: 0.8729 (m-10) cc_final: 0.8450 (m-10) REVERT: M 236 GLU cc_start: 0.7692 (tp30) cc_final: 0.7431 (tp30) REVERT: H 30 TYR cc_start: 0.8700 (t80) cc_final: 0.8335 (t80) REVERT: H 43 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6738 (mm-30) REVERT: H 52 ASN cc_start: 0.8816 (p0) cc_final: 0.8436 (p0) REVERT: H 60 LYS cc_start: 0.7647 (mmpt) cc_final: 0.6943 (mttp) REVERT: H 122 GLU cc_start: 0.7344 (tt0) cc_final: 0.7063 (tt0) REVERT: H 182 GLU cc_start: 0.8620 (tt0) cc_final: 0.8034 (tt0) REVERT: B 17 GLN cc_start: 0.8142 (mt0) cc_final: 0.7768 (mt0) REVERT: B 24 MET cc_start: 0.8592 (tpp) cc_final: 0.8209 (mmt) REVERT: F 15 ARG cc_start: 0.8209 (mtp85) cc_final: 0.8001 (mtp-110) REVERT: G 6 LEU cc_start: 0.3327 (OUTLIER) cc_final: 0.2917 (pp) REVERT: G 43 ILE cc_start: 0.8534 (mt) cc_final: 0.8300 (mm) REVERT: O 6 LYS cc_start: 0.8074 (mtmp) cc_final: 0.7508 (mttm) REVERT: P 25 SER cc_start: 0.8620 (t) cc_final: 0.8334 (p) REVERT: P 29 LEU cc_start: 0.8349 (tp) cc_final: 0.7699 (tp) REVERT: Q 5 TYR cc_start: 0.8264 (p90) cc_final: 0.7816 (p90) REVERT: Q 6 LYS cc_start: 0.8382 (mttm) cc_final: 0.8137 (mttm) REVERT: Q 20 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7285 (mm-40) REVERT: R 18 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: S 3 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8049 (mtpp) REVERT: T 35 ILE cc_start: 0.8561 (mt) cc_final: 0.8351 (mm) REVERT: V 20 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: V 45 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8092 (mm-30) REVERT: W 24 MET cc_start: 0.8109 (mmm) cc_final: 0.7823 (mmm) REVERT: Z 15 GLN cc_start: 0.7805 (mt0) cc_final: 0.7372 (mt0) REVERT: 2 29 LEU cc_start: 0.8451 (tp) cc_final: 0.8216 (tt) REVERT: 3 5 TYR cc_start: 0.7315 (p90) cc_final: 0.7087 (p90) REVERT: 5 15 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.4508 (tmt170) REVERT: 5 30 MET cc_start: 0.8125 (ttp) cc_final: 0.7872 (ttp) REVERT: 5 53 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7674 (ttm170) REVERT: 6 13 ASP cc_start: 0.5982 (t0) cc_final: 0.5256 (t70) REVERT: 7 51 TYR cc_start: 0.7399 (m-80) cc_final: 0.6999 (m-80) REVERT: 8 30 PHE cc_start: 0.6413 (t80) cc_final: 0.6104 (t80) REVERT: X 53 ARG cc_start: 0.7353 (mtm110) cc_final: 0.6644 (mtt90) REVERT: X 54 MET cc_start: 0.7892 (ptm) cc_final: 0.7504 (ptt) REVERT: X 59 GLU cc_start: 0.6561 (mp0) cc_final: 0.6313 (mp0) REVERT: U 24 MET cc_start: 0.7656 (ptp) cc_final: 0.7455 (ptp) outliers start: 41 outliers final: 25 residues processed: 316 average time/residue: 0.5473 time to fit residues: 203.2736 Evaluate side-chains 314 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 3 residue 10 ILE Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 15 ARG Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 125 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 39 optimal weight: 0.0050 chunk 52 optimal weight: 0.8980 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.100090 restraints weight = 27824.112| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.21 r_work: 0.2805 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24351 Z= 0.173 Angle : 0.710 16.618 33239 Z= 0.280 Chirality : 0.039 0.254 3335 Planarity : 0.004 0.056 3930 Dihedral : 16.552 179.699 4498 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.20 % Allowed : 17.74 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.36 (0.17), residues: 2199 helix: 2.44 (0.12), residues: 1518 sheet: 0.68 (0.97), residues: 34 loop : -0.57 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.026 0.002 TYR O 5 PHE 0.015 0.001 PHE M 216 TRP 0.019 0.002 TRP P 28 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (24319) covalent geometry : angle 0.70977 / 0.28 (33239) hydrogen bonds : bond 0.04777 / 3.23 ( 1269) hydrogen bonds : angle 3.47515 / 2.48 ( 3600) Misc. bond : bond 0.00272 / 0.17 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7368.77 seconds wall clock time: 126 minutes 35.44 seconds (7595.44 seconds total)