Starting phenix.real_space_refine on Tue Jul 7 03:50:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7va9_31835/07_2026/7va9_31835.cif Found real_map, /net/cci-nas-00/data/ceres_data/7va9_31835/07_2026/7va9_31835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7va9_31835/07_2026/7va9_31835.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7va9_31835/07_2026/7va9_31835.cif" model { file = "/net/cci-nas-00/data/ceres_data/7va9_31835/07_2026/7va9_31835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7va9_31835/07_2026/7va9_31835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7va9_31835/07_2026/7va9_31835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7va9_31835/07_2026/7va9_31835.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 15 5.49 5 Mg 64 5.21 5 S 162 5.16 5 C 29574 2.51 5 N 5997 2.21 5 O 6362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.04s 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: 42176 Number of models: 1 Model: "" Number of chains: 124 Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2431 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "H" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1972 Classifications: {'peptide': 260} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "G" 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: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 316 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 316 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "Q" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "R" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 316 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "S" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "T" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 316 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "U" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "V" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "W" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "X" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "Y" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "Z" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "1" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "2" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 297 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "7" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "8" 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: "9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "0" 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: "C" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 507 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "l" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2431 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "h" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1972 Classifications: {'peptide': 260} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "a" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "g" 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: "i" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "n" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "o" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "p" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "q" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "r" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "s" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "t" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "u" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "v" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "w" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "x" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "y" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "z" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "5" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "4" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 297 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "6" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "aa" 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: "3" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "ab" 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: "c" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 507 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "L" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 335 Unusual residues: {'BCL': 2, 'BPB': 2, 'PC1': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 376 Unusual residues: {'BCL': 2, 'CDL': 1, 'FE2': 1, 'PC1': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 205 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "B" 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: "D" 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: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "F" 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: "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: 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: "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: 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: "N" 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: "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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'SPO:plan-4': 1} Unresolved non-hydrogen planarities: 4 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'SPO:plan-4': 1} Unresolved non-hydrogen planarities: 4 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: "U" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 154 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "W" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "X" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "Y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "2" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 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: "9" 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: "0" 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: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 360 Unusual residues: {'BCL': 2, 'BPB': 2, 'PC1': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 323 Unusual residues: {'BCL': 2, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "h" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "a" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 197 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 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: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "e" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'SPO:plan-4': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "g" 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: "i" 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: "j" 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: "k" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 164 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'SPO:plan-3': 1, 'SPO:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "o" 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: "p" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "q" 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: "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: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 238 Unusual residues: {'BCL': 2, 'SPO': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "t" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "x" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "5" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "aa" 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: "3" 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: "ab" 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: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.39, per 1000 atoms: 0.22 Number of scatterers: 42176 At special positions: 0 Unit cell: (226.18, 136.702, 126.76, 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 2 26.01 S 162 16.00 P 15 15.00 Mg 64 11.99 O 6362 8.00 N 5997 7.00 C 29574 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=27, symmetry=0 Number of additional bonds: simple=27, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.6 seconds 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8136 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 12 sheets defined 73.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 31 through 57 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.521A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.712A 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: 3.590A pdb=" N TYR L 144 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 164 removed outlier: 3.738A pdb=" N ASP L 155 " --> pdb=" O TRP L 151 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 169 removed outlier: 5.847A 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 220 Processing helix chain 'L' and resid 225 through 250 Processing helix chain 'L' and resid 258 through 268 removed outlier: 3.571A pdb=" N TRP L 262 " --> pdb=" O GLN L 258 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 41 removed outlier: 3.579A pdb=" N TRP M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) 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 108 through 111 Processing helix chain 'M' and resid 112 through 140 removed outlier: 3.805A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.713A pdb=" N GLU M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 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: 3.532A pdb=" N GLU M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 290 removed outlier: 3.794A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLY M 288 " --> pdb=" O ILE M 284 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR M 289 " --> pdb=" O LEU M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'H' and resid 11 through 35 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 removed outlier: 3.590A pdb=" N ALA H 112 " --> pdb=" O VAL H 109 " (cutoff:3.500A) 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 214 removed outlier: 4.123A pdb=" N ALA H 214 " --> pdb=" O SER H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 removed outlier: 4.195A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 260 Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.533A pdb=" N THR A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'B' and resid 13 through 46 Processing helix chain 'D' and resid 3 through 10 Processing helix chain 'D' and resid 12 through 38 removed outlier: 3.545A pdb=" N THR D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'E' and resid 13 through 46 Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 12 through 38 removed outlier: 3.519A pdb=" N THR F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'G' and resid 13 through 46 Processing helix chain 'I' and resid 3 through 10 Processing helix chain 'I' and resid 12 through 38 removed outlier: 3.518A pdb=" N THR I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 51 Processing helix chain 'J' and resid 13 through 46 Processing helix chain 'K' and resid 3 through 10 Processing helix chain 'K' and resid 12 through 38 removed outlier: 3.528A pdb=" N THR K 38 " --> pdb=" O ILE K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 52 Processing helix chain 'N' and resid 13 through 46 Processing helix chain 'O' and resid 3 through 10 Processing helix chain 'O' and resid 12 through 38 removed outlier: 3.535A pdb=" N THR O 38 " --> pdb=" O ILE O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 51 removed outlier: 3.905A pdb=" N TYR O 51 " --> pdb=" O SER O 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 46 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 12 through 38 removed outlier: 3.536A pdb=" N THR Q 38 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 52 Processing helix chain 'R' and resid 13 through 46 Processing helix chain 'S' and resid 3 through 10 Processing helix chain 'S' and resid 12 through 38 removed outlier: 3.541A pdb=" N THR S 38 " --> pdb=" O ILE S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 52 Processing helix chain 'T' and resid 13 through 46 Processing helix chain 'U' and resid 12 through 38 removed outlier: 3.567A pdb=" N THR U 38 " --> pdb=" O ILE U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 51 Processing helix chain 'V' and resid 14 through 46 Processing helix chain 'W' and resid 13 through 38 removed outlier: 3.568A pdb=" N THR W 38 " --> pdb=" O ILE W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 51 Processing helix chain 'X' and resid 14 through 46 Processing helix chain 'Y' and resid 13 through 38 removed outlier: 3.568A pdb=" N THR Y 38 " --> pdb=" O ILE Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 51 Processing helix chain 'Z' and resid 14 through 46 Processing helix chain '1' and resid 13 through 38 removed outlier: 3.567A pdb=" N THR 1 38 " --> pdb=" O ILE 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 51 Processing helix chain '2' and resid 14 through 46 Processing helix chain '7' and resid 3 through 10 Processing helix chain '7' and resid 12 through 38 removed outlier: 3.640A pdb=" N THR 7 38 " --> pdb=" O ILE 7 34 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 46 Processing helix chain '9' and resid 3 through 10 Processing helix chain '9' and resid 12 through 38 removed outlier: 3.547A pdb=" N THR 9 38 " --> pdb=" O ILE 9 34 " (cutoff:3.500A) Processing helix chain '9' and resid 42 through 51 Processing helix chain '0' and resid 13 through 46 Processing helix chain 'C' and resid 14 through 55 Processing helix chain 'C' and resid 56 through 59 removed outlier: 3.718A pdb=" N GLU C 59 " --> pdb=" O PRO C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 59' Processing helix chain 'l' and resid 6 through 10 Processing helix chain 'l' and resid 31 through 57 Processing helix chain 'l' and resid 70 through 74 Processing helix chain 'l' and resid 79 through 82 Processing helix chain 'l' and resid 83 through 112 Processing helix chain 'l' and resid 115 through 133 removed outlier: 3.521A pdb=" N PHE l 123 " --> pdb=" O PHE l 119 " (cutoff:3.500A) removed outlier: 3.712A 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: 3.591A pdb=" N TYR l 144 " --> pdb=" O ALA l 141 " (cutoff:3.500A) Processing helix chain 'l' and resid 151 through 164 removed outlier: 3.740A pdb=" N ASP l 155 " --> pdb=" O TRP l 151 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 165 through 169 removed outlier: 5.849A 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 220 Processing helix chain 'l' and resid 225 through 250 Processing helix chain 'l' and resid 258 through 268 removed outlier: 3.570A pdb=" N TRP l 262 " --> pdb=" O GLN l 258 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP l 265 " --> pdb=" O ASP l 261 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP l 266 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 41 removed outlier: 3.579A pdb=" N TRP m 41 " --> pdb=" O THR m 37 " (cutoff:3.500A) 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 108 through 111 Processing helix chain 'm' and resid 112 through 140 removed outlier: 3.803A pdb=" N LEU m 140 " --> pdb=" O ARG m 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 144 through 162 Processing helix chain 'm' and resid 162 through 169 Processing helix chain 'm' and resid 170 through 174 removed outlier: 3.713A pdb=" N GLU m 173 " --> pdb=" O SER m 170 " (cutoff:3.500A) Processing helix chain 'm' and resid 178 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: 3.532A pdb=" N GLU m 246 " --> pdb=" O GLY m 242 " (cutoff:3.500A) Processing helix chain 'm' and resid 263 through 290 removed outlier: 3.793A pdb=" N ARG m 267 " --> pdb=" O GLU m 263 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLY m 288 " --> pdb=" O ILE m 284 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR m 289 " --> pdb=" O LEU m 285 " (cutoff:3.500A) Processing helix chain 'm' and resid 293 through 301 Processing helix chain 'h' and resid 11 through 35 Processing helix chain 'h' and resid 103 through 108 Processing helix chain 'h' and resid 109 through 113 removed outlier: 3.592A pdb=" N ALA h 112 " --> pdb=" O VAL h 109 " (cutoff:3.500A) 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 214 removed outlier: 4.125A pdb=" N ALA h 214 " --> pdb=" O SER h 210 " (cutoff:3.500A) Processing helix chain 'h' and resid 226 through 244 removed outlier: 4.196A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 250 through 260 Processing helix chain 'a' and resid 3 through 10 Processing helix chain 'a' and resid 12 through 38 removed outlier: 3.541A pdb=" N THR a 38 " --> pdb=" O ILE a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 51 Processing helix chain 'b' and resid 13 through 46 Processing helix chain 'd' and resid 3 through 10 Processing helix chain 'd' and resid 12 through 38 removed outlier: 3.545A pdb=" N THR d 38 " --> pdb=" O ILE d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 51 Processing helix chain 'e' and resid 13 through 46 Processing helix chain 'f' and resid 3 through 10 Processing helix chain 'f' and resid 12 through 38 removed outlier: 3.535A pdb=" N THR f 38 " --> pdb=" O ILE f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 51 Processing helix chain 'g' and resid 13 through 46 Processing helix chain 'i' and resid 3 through 10 Processing helix chain 'i' and resid 12 through 38 removed outlier: 3.523A pdb=" N THR i 38 " --> pdb=" O ILE i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 42 through 51 Processing helix chain 'j' and resid 13 through 46 Processing helix chain 'k' and resid 3 through 10 Processing helix chain 'k' and resid 12 through 38 removed outlier: 3.530A pdb=" N THR k 38 " --> pdb=" O ILE k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 42 through 51 Processing helix chain 'n' and resid 14 through 46 Processing helix chain 'o' and resid 3 through 10 Processing helix chain 'o' and resid 12 through 38 removed outlier: 3.558A pdb=" N THR o 38 " --> pdb=" O ILE o 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 51 removed outlier: 3.579A pdb=" N TYR o 51 " --> pdb=" O SER o 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 14 through 46 Processing helix chain 'q' and resid 3 through 10 Processing helix chain 'q' and resid 12 through 38 removed outlier: 3.538A pdb=" N THR q 38 " --> pdb=" O ILE q 34 " (cutoff:3.500A) Processing helix chain 'q' and resid 42 through 51 Processing helix chain 'r' and resid 14 through 46 Processing helix chain 's' and resid 3 through 10 Processing helix chain 's' and resid 12 through 38 removed outlier: 3.521A pdb=" N THR s 38 " --> pdb=" O ILE s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 52 Processing helix chain 't' and resid 14 through 46 removed outlier: 3.662A pdb=" N VAL t 23 " --> pdb=" O GLU t 19 " (cutoff:3.500A) Processing helix chain 'u' and resid 12 through 38 removed outlier: 3.567A pdb=" N THR u 38 " --> pdb=" O ILE u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 42 through 51 Processing helix chain 'v' and resid 14 through 46 Processing helix chain 'w' and resid 13 through 38 removed outlier: 3.569A pdb=" N THR w 38 " --> pdb=" O ILE w 34 " (cutoff:3.500A) Processing helix chain 'w' and resid 42 through 51 Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 13 through 38 removed outlier: 3.569A pdb=" N THR y 38 " --> pdb=" O ILE y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 42 through 51 Processing helix chain 'z' and resid 14 through 46 Processing helix chain '5' and resid 13 through 38 removed outlier: 3.569A pdb=" N THR 5 38 " --> pdb=" O ILE 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 51 Processing helix chain '4' and resid 14 through 46 Processing helix chain '6' and resid 3 through 10 Processing helix chain '6' and resid 12 through 38 removed outlier: 3.708A pdb=" N THR 6 38 " --> pdb=" O ILE 6 34 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 46 removed outlier: 3.836A pdb=" N GLU 6 45 " --> pdb=" O ASN 6 42 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE 6 46 " --> pdb=" O TRP 6 43 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 42 through 46' Processing helix chain 'aa' and resid 13 through 46 Processing helix chain '3' and resid 3 through 10 Processing helix chain '3' and resid 12 through 38 removed outlier: 3.557A pdb=" N THR 3 38 " --> pdb=" O ILE 3 34 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 51 Processing helix chain 'ab' and resid 13 through 46 Processing helix chain 'c' and resid 14 through 55 Processing helix chain 'c' and resid 56 through 59 removed outlier: 3.718A pdb=" N GLU c 59 " --> pdb=" O PRO c 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 56 through 59' Processing sheet with id=AA1, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.473A pdb=" N GLN M 11 " --> pdb=" O SER H 143 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG M 13 " --> pdb=" O HIS H 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 62 through 66 removed outlier: 4.493A pdb=" N GLY H 71 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.671A pdb=" N VAL H 164 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL H 181 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP H 166 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU H 179 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP H 168 " --> pdb=" O ARG H 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET H 175 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.786A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'l' and resid 25 through 26 Processing sheet with id=AA8, first strand: chain 'm' and resid 10 through 13 removed outlier: 6.230A pdb=" N GLN m 11 " --> pdb=" O SER h 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'h' and resid 62 through 66 removed outlier: 4.494A pdb=" N GLY h 71 " --> pdb=" O LEU h 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'h' and resid 87 through 89 Processing sheet with id=AB2, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.672A pdb=" N VAL h 164 " --> pdb=" O VAL h 181 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL h 181 " --> pdb=" O VAL h 164 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP h 166 " --> pdb=" O LEU h 179 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU h 179 " --> pdb=" O ASP h 166 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP h 168 " --> pdb=" O ARG h 177 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET h 175 " --> pdb=" O ASP h 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 131 through 133 removed outlier: 3.784A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 2494 hydrogen bonds defined for protein. 7074 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: 6.67 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.34: 11179 1.34 - 1.55: 31824 1.55 - 1.76: 269 1.76 - 1.97: 311 1.97 - 2.17: 256 Bond restraints: 43839 Sorted by residual: bond pdb=" C3C BPB l 306 " pdb=" CAC BPB l 306 " ideal model delta sigma weight residual 1.334 1.551 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C3C BPB L 305 " pdb=" CAC BPB L 305 " ideal model delta sigma weight residual 1.334 1.550 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C32 SPO s 105 " pdb=" C33 SPO s 105 " ideal model delta sigma weight residual 1.336 1.544 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C37 SPO s 104 " pdb=" C38 SPO s 104 " ideal model delta sigma weight residual 1.336 1.542 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C37 SPO 8 101 " pdb=" C38 SPO 8 101 " ideal model delta sigma weight residual 1.336 1.541 -0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 43834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 58498 4.79 - 9.58: 950 9.58 - 14.37: 523 14.37 - 19.17: 349 19.17 - 23.96: 19 Bond angle restraints: 60339 Sorted by residual: angle pdb=" C12 SPO e 103 " pdb=" C14 SPO e 103 " pdb=" C15 SPO e 103 " ideal model delta sigma weight residual 127.13 103.17 23.96 3.00e+00 1.11e-01 6.38e+01 angle pdb=" C10 SPO i 102 " pdb=" C9 SPO i 102 " pdb=" C7 SPO i 102 " ideal model delta sigma weight residual 127.14 103.22 23.92 3.00e+00 1.11e-01 6.36e+01 angle pdb=" C10 SPO e 103 " pdb=" C9 SPO e 103 " pdb=" C7 SPO e 103 " ideal model delta sigma weight residual 127.14 104.51 22.63 3.00e+00 1.11e-01 5.69e+01 angle pdb=" CB ARG h 177 " pdb=" CG ARG h 177 " pdb=" CD ARG h 177 " ideal model delta sigma weight residual 111.30 94.67 16.63 2.30e+00 1.89e-01 5.23e+01 angle pdb=" CB ARG H 177 " pdb=" CG ARG H 177 " pdb=" CD ARG H 177 " ideal model delta sigma weight residual 111.30 94.79 16.51 2.30e+00 1.89e-01 5.16e+01 ... (remaining 60334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 22184 35.93 - 71.86: 869 71.86 - 107.79: 66 107.79 - 143.72: 20 143.72 - 179.65: 5 Dihedral angle restraints: 23144 sinusoidal: 10524 harmonic: 12620 Sorted by residual: dihedral pdb=" C1 BCL m1301 " pdb=" C2 BCL m1301 " pdb=" C3 BCL m1301 " pdb=" C5 BCL m1301 " ideal model delta sinusoidal sigma weight residual -180.00 -0.35 -179.65 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL M1301 " pdb=" C2 BCL M1301 " pdb=" C3 BCL M1301 " pdb=" C5 BCL M1301 " ideal model delta sinusoidal sigma weight residual -180.00 -0.46 -179.54 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" CA GLU l 201 " pdb=" C GLU l 201 " pdb=" N LYS l 202 " pdb=" CA LYS l 202 " ideal model delta harmonic sigma weight residual 180.00 -131.67 -48.33 0 5.00e+00 4.00e-02 9.34e+01 ... (remaining 23141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 5521 0.090 - 0.181: 377 0.181 - 0.271: 17 0.271 - 0.361: 4 0.361 - 0.452: 1 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CB THR o 38 " pdb=" CA THR o 38 " pdb=" OG1 THR o 38 " pdb=" CG2 THR o 38 " both_signs ideal model delta sigma weight residual False 2.55 2.10 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CG LEU h 241 " pdb=" CB LEU h 241 " pdb=" CD1 LEU h 241 " pdb=" CD2 LEU h 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CG LEU H 241 " pdb=" CB LEU H 241 " pdb=" CD1 LEU H 241 " pdb=" CD2 LEU H 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 5917 not shown) Planarity restraints: 7401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C31 SPO 9 102 " 0.541 2.00e-02 2.50e+03 4.85e-01 2.95e+03 pdb=" C32 SPO 9 102 " -0.669 2.00e-02 2.50e+03 pdb=" C33 SPO 9 102 " -0.468 2.00e-02 2.50e+03 pdb=" C34 SPO 9 102 " 0.444 2.00e-02 2.50e+03 pdb=" C35 SPO 9 102 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C31 SPO 3 101 " -0.541 2.00e-02 2.50e+03 4.85e-01 2.94e+03 pdb=" C32 SPO 3 101 " 0.665 2.00e-02 2.50e+03 pdb=" C33 SPO 3 101 " 0.471 2.00e-02 2.50e+03 pdb=" C34 SPO 3 101 " -0.447 2.00e-02 2.50e+03 pdb=" C35 SPO 3 101 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C31 SPO D 102 " 0.538 2.00e-02 2.50e+03 4.84e-01 2.93e+03 pdb=" C32 SPO D 102 " -0.662 2.00e-02 2.50e+03 pdb=" C33 SPO D 102 " -0.473 2.00e-02 2.50e+03 pdb=" C34 SPO D 102 " 0.448 2.00e-02 2.50e+03 pdb=" C35 SPO D 102 " 0.148 2.00e-02 2.50e+03 ... (remaining 7398 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 321 2.57 - 3.16: 32226 3.16 - 3.74: 66640 3.74 - 4.32: 97781 4.32 - 4.90: 158563 Nonbonded interactions: 355531 Sorted by model distance: nonbonded pdb=" OG1 THR K 38 " pdb=" O SER K 40 " model vdw 1.992 3.040 nonbonded pdb=" OH TYR y 41 " pdb=" OG SER 5 47 " model vdw 2.018 3.040 nonbonded pdb=" O LYS 7 3 " pdb=" NZ LYS 7 6 " model vdw 2.028 3.120 nonbonded pdb=" OE1 GLN f 20 " pdb=" OH TYR g 24 " model vdw 2.058 3.040 nonbonded pdb=" OE1 GLN s 20 " pdb=" OH TYR t 24 " model vdw 2.078 3.040 ... (remaining 355526 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 12 through 49) selection = (chain '8' and resid 12 through 49) selection = (chain 'B' and resid 12 through 49) selection = (chain 'E' and resid 12 through 49) selection = (chain 'G' and resid 12 through 49) selection = (chain 'J' and resid 12 through 49) selection = (chain 'N' and resid 12 through 49) selection = (chain 'R' and resid 12 through 49) selection = (chain 'T' and resid 12 through 49) selection = (chain 'aa' and resid 12 through 49) selection = (chain 'ab' and resid 12 through 49) selection = (chain 'b' and resid 12 through 49) selection = (chain 'e' and resid 12 through 49) selection = (chain 'g' and resid 12 through 49) selection = (chain 'j' and resid 12 through 49) } ncs_group { reference = chain '1' selection = (chain '5' and resid 12 through 101) selection = (chain 'U' and (resid 12 through 54 or (resid 101 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )))) selection = chain 'W' selection = chain 'Y' selection = (chain 'u' and (resid 12 through 54 or (resid 101 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )))) selection = chain 'w' selection = chain 'y' } ncs_group { reference = (chain '2' and resid 13 through 48) selection = chain '4' selection = (chain 'P' and resid 13 through 48) selection = (chain 'V' and resid 13 through 48) selection = (chain 'X' and resid 13 through 48) selection = (chain 'Z' and resid 13 through 48) selection = (chain 'n' and resid 13 through 48) selection = (chain 'p' and resid 13 through 48) selection = (chain 'r' and resid 13 through 48) selection = (chain 't' and resid 13 through 48) selection = (chain 'v' and resid 13 through 48) selection = (chain 'x' and resid 13 through 48) selection = (chain 'z' and resid 13 through 48) } ncs_group { reference = (chain '3' and resid 1 through 54) selection = (chain '9' and resid 1 through 54) selection = (chain 'A' and resid 1 through 54) selection = (chain 'D' and resid 1 through 54) selection = (chain 'F' and resid 1 through 54) selection = (chain 'I' and resid 1 through 54) selection = (chain 'K' and resid 1 through 54) selection = (chain 'O' and resid 1 through 54) selection = (chain 'Q' and resid 1 through 54) selection = (chain 'S' and resid 1 through 54) selection = (chain 'a' and resid 1 through 54) selection = (chain 'd' and resid 1 through 54) selection = (chain 'f' and resid 1 through 54) selection = (chain 'i' and resid 1 through 54) selection = (chain 'k' and resid 1 through 54) selection = (chain 'o' and resid 1 through 54) selection = (chain 'q' and resid 1 through 54) selection = (chain 's' and resid 1 through 54) } ncs_group { reference = chain '6' selection = (chain '7' and resid 1 through 46) } ncs_group { reference = (chain 'C' and resid 5 through 69) selection = (chain 'c' and resid 5 through 69) } ncs_group { reference = chain 'H' selection = (chain 'h' and resid 1 through 260) } ncs_group { reference = (chain 'L' and resid 1 through 303) selection = (chain 'l' and (resid 1 through 302 or (resid 303 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C1M or name C2 or name C20 or name C21 or name C2 \ 2 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or nam \ e C29 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C3M or name C4 or name C4M or name C5 or name C6 or \ name C7 or name C8 or name C9 or name O2 or name O3 or name O4 or name O5 )))) } ncs_group { reference = (chain 'M' and resid 2 through 1306) selection = chain 'm' } 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: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 33.190 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.538 43866 Z= 1.453 Angle : 2.121 23.957 60339 Z= 0.780 Chirality : 0.049 0.452 5920 Planarity : 0.051 0.485 7401 Dihedral : 18.344 179.655 15008 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.83 % Allowed : 2.36 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.34 (0.13), residues: 4222 helix: 1.99 (0.09), residues: 2880 sheet: -1.66 (0.67), residues: 46 loop : -1.64 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG D 15 TYR 0.066 0.003 TYR H 236 PHE 0.080 0.003 PHE m 216 TRP 0.062 0.003 TRP L 272 HIS 0.011 0.002 HIS p 39 Details of bonding type rmsd/Z covalent geometry : bond 0.01954 / 0.96 (43839) covalent geometry : angle 2.12141 / 0.78 (60339) hydrogen bonds : bond 0.10950 / 7.36 ( 2490) hydrogen bonds : angle 4.42745 / 3.17 ( 7074) Misc. bond : bond 0.43946 / 27.40 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 698 time to evaluate : 1.411 Fit side-chains REVERT: J 40 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8212 (mm) REVERT: W 26 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6253 (tp) REVERT: C 61 GLN cc_start: 0.7258 (tp40) cc_final: 0.6794 (tp40) REVERT: l 47 ILE cc_start: 0.8230 (mm) cc_final: 0.8002 (mm) REVERT: m 2 GLU cc_start: 0.4637 (tt0) cc_final: 0.4083 (tt0) REVERT: m 4 GLN cc_start: 0.8659 (mm110) cc_final: 0.8259 (mm110) REVERT: h 81 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5119 (mt-10) REVERT: k 1 MET cc_start: 0.5215 (tmm) cc_final: 0.4765 (tmm) REVERT: 6 2 SER cc_start: 0.7303 (p) cc_final: 0.6946 (m) outliers start: 103 outliers final: 6 residues processed: 744 average time/residue: 0.2285 time to fit residues: 284.0476 Evaluate side-chains 534 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 525 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain M residue 287 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain h residue 4 VAL Chi-restraints excluded: chain h residue 81 GLU Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain 5 residue 30 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 199 GLN b 16 GLN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 42 ASN r 21 HIS s 20 GLN ** y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aa 16 GLN ab 18 GLN c 66 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.173616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.139418 restraints weight = 46294.194| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.80 r_work: 0.3137 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43866 Z= 0.148 Angle : 0.811 15.592 60339 Z= 0.321 Chirality : 0.038 0.207 5920 Planarity : 0.005 0.056 7401 Dihedral : 16.826 179.988 7346 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.02 % Allowed : 5.55 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.30 (0.12), residues: 4222 helix: 2.82 (0.09), residues: 2780 sheet: -1.50 (0.69), residues: 46 loop : -1.19 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG h 177 TYR 0.039 0.002 TYRaa 24 PHE 0.040 0.002 PHE m 216 TRP 0.019 0.001 TRP L 272 HIS 0.010 0.001 HIS x 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (43839) covalent geometry : angle 0.81122 / 0.32 (60339) hydrogen bonds : bond 0.05434 / 3.60 ( 2490) hydrogen bonds : angle 3.67551 / 2.62 ( 7074) Misc. bond : bond 0.00253 / 0.15 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 602 time to evaluate : 1.504 Fit side-chains REVERT: H 38 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7880 (mm-30) REVERT: A 45 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6901 (mm-30) REVERT: F 3 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7248 (mptt) REVERT: I 1 MET cc_start: 0.1876 (tpt) cc_final: 0.1217 (tmm) REVERT: I 3 LYS cc_start: 0.6612 (mttp) cc_final: 0.6164 (mttm) REVERT: I 30 MET cc_start: 0.6505 (ttm) cc_final: 0.6014 (tpp) REVERT: N 40 LEU cc_start: 0.8637 (mp) cc_final: 0.8415 (mp) REVERT: O 45 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6574 (mm-30) REVERT: Q 30 MET cc_start: 0.8284 (ttt) cc_final: 0.8080 (ttt) REVERT: W 26 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6515 (tp) REVERT: W 41 TYR cc_start: 0.6659 (m-80) cc_final: 0.6210 (m-80) REVERT: 7 6 LYS cc_start: 0.7851 (ptpt) cc_final: 0.7472 (mtpt) REVERT: 9 3 LYS cc_start: 0.7246 (ptpt) cc_final: 0.7029 (mtpp) REVERT: C 27 MET cc_start: 0.8386 (mtt) cc_final: 0.8034 (mtt) REVERT: m 26 LEU cc_start: 0.8207 (mp) cc_final: 0.7917 (mp) REVERT: m 68 PHE cc_start: 0.8553 (t80) cc_final: 0.8335 (t80) REVERT: h 220 LYS cc_start: 0.7194 (ttpp) cc_final: 0.6727 (tmmt) REVERT: a 52 ASN cc_start: 0.7616 (OUTLIER) cc_final: 0.7383 (m-40) REVERT: b 40 LEU cc_start: 0.8260 (mt) cc_final: 0.7925 (tp) REVERT: i 1 MET cc_start: 0.3096 (tmm) cc_final: 0.2610 (tpp) REVERT: i 9 MET cc_start: 0.6467 (mtm) cc_final: 0.6006 (mtp) REVERT: q 9 MET cc_start: 0.6809 (mtm) cc_final: 0.6442 (mpp) REVERT: s 9 MET cc_start: 0.5425 (mmp) cc_final: 0.5195 (mmp) REVERT: z 25 MET cc_start: 0.2910 (mtm) cc_final: 0.1914 (tmm) REVERT: ab 13 THR cc_start: 0.8110 (p) cc_final: 0.7900 (m) outliers start: 37 outliers final: 19 residues processed: 625 average time/residue: 0.2466 time to fit residues: 258.4620 Evaluate side-chains 565 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 543 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 52 ASN Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain ab residue 26 SER Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 257 optimal weight: 3.9990 chunk 343 optimal weight: 0.9980 chunk 260 optimal weight: 4.9990 chunk 263 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 292 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 324 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 373 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 183 ASN ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 GLN ab 18 GLN c 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.168326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.140428 restraints weight = 46046.000| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.42 r_work: 0.3133 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 43866 Z= 0.212 Angle : 0.842 14.863 60339 Z= 0.333 Chirality : 0.042 0.154 5920 Planarity : 0.005 0.058 7401 Dihedral : 16.494 179.960 7332 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.65 % Allowed : 7.48 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.21 (0.12), residues: 4222 helix: 2.63 (0.09), residues: 2786 sheet: -1.48 (0.68), residues: 46 loop : -0.97 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGab 46 TYR 0.037 0.002 TYR G 24 PHE 0.035 0.002 PHE m 216 TRP 0.027 0.002 TRP l 272 HIS 0.010 0.002 HIS m 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 (43839) covalent geometry : angle 0.84199 / 0.33 (60339) hydrogen bonds : bond 0.06187 / 4.10 ( 2490) hydrogen bonds : angle 3.74978 / 2.67 ( 7074) Misc. bond : bond 0.00254 / 0.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 572 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: M 86 LEU cc_start: 0.7761 (tt) cc_final: 0.7449 (mt) REVERT: M 135 LEU cc_start: 0.8994 (mt) cc_final: 0.8777 (mt) REVERT: H 38 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7650 (mm-30) REVERT: H 74 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8402 (t) REVERT: H 103 ASP cc_start: 0.7700 (t70) cc_final: 0.7490 (t70) REVERT: F 3 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7427 (mptt) REVERT: F 30 MET cc_start: 0.8495 (tpp) cc_final: 0.8220 (ttt) REVERT: I 44 LEU cc_start: 0.8445 (mt) cc_final: 0.8160 (mt) REVERT: N 40 LEU cc_start: 0.8707 (mp) cc_final: 0.8489 (mp) REVERT: W 26 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6791 (tp) REVERT: 7 6 LYS cc_start: 0.8239 (ptpt) cc_final: 0.7843 (mtpt) REVERT: m 86 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7531 (tp) REVERT: h 197 LYS cc_start: 0.8048 (tptt) cc_final: 0.7508 (ttpt) REVERT: h 220 LYS cc_start: 0.7166 (ttpp) cc_final: 0.6705 (tmmt) REVERT: h 228 LEU cc_start: 0.8232 (tp) cc_final: 0.8000 (tp) REVERT: h 247 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6344 (pttt) REVERT: d 30 MET cc_start: 0.8722 (ttt) cc_final: 0.8498 (ttm) REVERT: i 1 MET cc_start: 0.3647 (tmm) cc_final: 0.3394 (tpp) REVERT: o 47 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7969 (p) REVERT: q 9 MET cc_start: 0.6752 (mtm) cc_final: 0.6363 (mpp) REVERT: s 9 MET cc_start: 0.5541 (mmp) cc_final: 0.5179 (mmp) REVERT: s 30 MET cc_start: 0.7639 (ttm) cc_final: 0.7390 (ttp) REVERT: u 45 GLU cc_start: 0.6411 (tt0) cc_final: 0.6138 (tp30) REVERT: y 30 MET cc_start: 0.4116 (ttt) cc_final: 0.3781 (ttp) REVERT: z 25 MET cc_start: 0.2898 (mtm) cc_final: 0.1809 (tmm) REVERT: 6 9 MET cc_start: 0.8738 (mtm) cc_final: 0.8486 (mtp) REVERT: ab 13 THR cc_start: 0.8275 (p) cc_final: 0.7955 (m) outliers start: 60 outliers final: 36 residues processed: 603 average time/residue: 0.2331 time to fit residues: 237.1233 Evaluate side-chains 578 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 536 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 195 ASN Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 247 LYS Chi-restraints excluded: chain a residue 45 GLU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain 6 residue 2 SER Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain ab residue 26 SER Chi-restraints excluded: chain c residue 66 ASN Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 392 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 chunk 340 optimal weight: 0.9990 chunk 234 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 GLN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 HIS 7 20 GLN C 66 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN 3 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.172567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.145449 restraints weight = 45780.448| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.42 r_work: 0.3226 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43866 Z= 0.122 Angle : 0.690 14.096 60339 Z= 0.270 Chirality : 0.036 0.139 5920 Planarity : 0.004 0.056 7401 Dihedral : 15.397 179.709 7332 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.35 % Allowed : 8.80 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.79 (0.12), residues: 4222 helix: 3.07 (0.09), residues: 2778 sheet: -1.15 (0.72), residues: 46 loop : -0.70 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 46 TYR 0.019 0.001 TYR E 24 PHE 0.024 0.001 PHE k 23 TRP 0.018 0.001 TRP l 271 HIS 0.008 0.001 HIS M 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (43839) covalent geometry : angle 0.68970 / 0.27 (60339) hydrogen bonds : bond 0.04960 / 3.28 ( 2490) hydrogen bonds : angle 3.48633 / 2.48 ( 7074) Misc. bond : bond 0.00147 / 0.09 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 570 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: M 86 LEU cc_start: 0.7851 (tt) cc_final: 0.7540 (mt) REVERT: A 45 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: F 3 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7475 (mptt) REVERT: F 30 MET cc_start: 0.8479 (tpp) cc_final: 0.8278 (ttt) REVERT: I 1 MET cc_start: 0.1955 (tpt) cc_final: 0.1253 (tmm) REVERT: I 30 MET cc_start: 0.6640 (ttm) cc_final: 0.6393 (tpt) REVERT: N 29 TRP cc_start: 0.6805 (m100) cc_final: 0.6291 (m100) REVERT: W 26 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6762 (tp) REVERT: l 59 TRP cc_start: 0.8394 (m100) cc_final: 0.8182 (m100) REVERT: m 234 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8177 (mt-10) REVERT: h 106 LYS cc_start: 0.7419 (mttt) cc_final: 0.7196 (mttm) REVERT: h 160 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7423 (mp) REVERT: h 197 LYS cc_start: 0.8159 (tptt) cc_final: 0.7601 (tttt) REVERT: h 220 LYS cc_start: 0.7109 (ttpp) cc_final: 0.6698 (tmmt) REVERT: h 231 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: i 9 MET cc_start: 0.6417 (mtm) cc_final: 0.6018 (mtp) REVERT: o 47 SER cc_start: 0.8257 (t) cc_final: 0.7969 (p) REVERT: q 9 MET cc_start: 0.6783 (mtm) cc_final: 0.6529 (mpp) REVERT: s 9 MET cc_start: 0.5395 (mmp) cc_final: 0.5045 (mmp) REVERT: s 30 MET cc_start: 0.7690 (ttm) cc_final: 0.7458 (ttp) REVERT: u 23 PHE cc_start: 0.7897 (t80) cc_final: 0.7340 (t80) REVERT: u 45 GLU cc_start: 0.6273 (tt0) cc_final: 0.5885 (tp30) REVERT: y 30 MET cc_start: 0.4214 (ttt) cc_final: 0.3829 (ttp) REVERT: z 25 MET cc_start: 0.2704 (mtm) cc_final: 0.1748 (tmm) REVERT: ab 13 THR cc_start: 0.8186 (p) cc_final: 0.7936 (m) outliers start: 49 outliers final: 28 residues processed: 597 average time/residue: 0.2443 time to fit residues: 246.3928 Evaluate side-chains 575 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 543 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain ab residue 26 SER Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 248 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 296 optimal weight: 1.9990 chunk 402 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 21 HIS ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN h 35 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 20 GLN 3 20 GLN c 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.168232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.141889 restraints weight = 45821.114| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.41 r_work: 0.3176 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 43866 Z= 0.183 Angle : 0.787 14.480 60339 Z= 0.309 Chirality : 0.040 0.145 5920 Planarity : 0.005 0.055 7401 Dihedral : 15.627 179.544 7332 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.90 % Allowed : 9.73 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 (0.12), residues: 4222 helix: 2.85 (0.09), residues: 2778 sheet: -1.25 (0.70), residues: 48 loop : -0.67 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 46 TYR 0.029 0.002 TYR F 41 PHE 0.020 0.002 PHE H 20 TRP 0.015 0.002 TRP l 271 HIS 0.026 0.002 HIS j 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (43839) covalent geometry : angle 0.78680 / 0.31 (60339) hydrogen bonds : bond 0.05823 / 3.86 ( 2490) hydrogen bonds : angle 3.62698 / 2.58 ( 7074) Misc. bond : bond 0.00262 / 0.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 544 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: M 86 LEU cc_start: 0.7920 (tt) cc_final: 0.7633 (mt) REVERT: H 38 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7663 (mm-30) REVERT: H 81 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.4529 (mm-30) REVERT: H 206 ASN cc_start: 0.8286 (t0) cc_final: 0.8079 (t0) REVERT: F 3 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7506 (mptt) REVERT: F 30 MET cc_start: 0.8618 (tpp) cc_final: 0.8327 (ttt) REVERT: I 30 MET cc_start: 0.7031 (ttm) cc_final: 0.6618 (tpt) REVERT: N 29 TRP cc_start: 0.6854 (m100) cc_final: 0.6326 (m100) REVERT: S 25 PHE cc_start: 0.8095 (t80) cc_final: 0.7716 (t80) REVERT: W 26 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6769 (tp) REVERT: 0 15 GLU cc_start: 0.6842 (pm20) cc_final: 0.6446 (pm20) REVERT: C 6 ILE cc_start: 0.4393 (OUTLIER) cc_final: 0.4096 (tp) REVERT: m 241 ARG cc_start: 0.8565 (ttp-170) cc_final: 0.8353 (ttp-170) REVERT: h 160 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7720 (mp) REVERT: h 191 LEU cc_start: 0.8488 (mt) cc_final: 0.8230 (tp) REVERT: h 197 LYS cc_start: 0.8245 (tptp) cc_final: 0.7725 (tttt) REVERT: h 220 LYS cc_start: 0.7192 (ttpp) cc_final: 0.6778 (tmmt) REVERT: h 228 LEU cc_start: 0.8319 (tp) cc_final: 0.8066 (tp) REVERT: h 231 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: k 1 MET cc_start: 0.6415 (tmm) cc_final: 0.5735 (tmm) REVERT: k 42 ASN cc_start: 0.8105 (t0) cc_final: 0.7841 (t0) REVERT: k 45 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6578 (mm-30) REVERT: o 47 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.8159 (p) REVERT: q 9 MET cc_start: 0.6809 (mtm) cc_final: 0.6508 (mpp) REVERT: s 30 MET cc_start: 0.7744 (ttm) cc_final: 0.7528 (ttp) REVERT: u 45 GLU cc_start: 0.6511 (tt0) cc_final: 0.6069 (tp30) REVERT: y 30 MET cc_start: 0.4136 (ttt) cc_final: 0.3806 (ttp) REVERT: z 25 MET cc_start: 0.2621 (mtm) cc_final: 0.1702 (tmm) REVERT: ab 13 THR cc_start: 0.8281 (p) cc_final: 0.7958 (m) outliers start: 69 outliers final: 45 residues processed: 586 average time/residue: 0.2377 time to fit residues: 235.0177 Evaluate side-chains 580 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 528 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 4 VAL Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 45 GLU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain y residue 42 ASN Chi-restraints excluded: chain 5 residue 30 MET Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 3 residue 30 MET Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain ab residue 26 SER Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 25 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 365 optimal weight: 0.9990 chunk 404 optimal weight: 5.9990 chunk 389 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN h 141 HIS ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 GLN c 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.169852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.143033 restraints weight = 45868.914| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.44 r_work: 0.3189 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 43866 Z= 0.151 Angle : 0.731 14.174 60339 Z= 0.287 Chirality : 0.038 0.146 5920 Planarity : 0.004 0.056 7401 Dihedral : 15.301 179.422 7332 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.03 % Allowed : 10.25 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.69 (0.12), residues: 4222 helix: 2.94 (0.09), residues: 2780 sheet: -1.12 (0.71), residues: 48 loop : -0.60 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 46 TYR 0.021 0.001 TYR A 41 PHE 0.018 0.001 PHE c 47 TRP 0.015 0.001 TRP l 271 HIS 0.009 0.001 HIS m 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (43839) covalent geometry : angle 0.73062 / 0.29 (60339) hydrogen bonds : bond 0.05387 / 3.57 ( 2490) hydrogen bonds : angle 3.55027 / 2.53 ( 7074) Misc. bond : bond 0.00209 / 0.13 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 550 time to evaluate : 1.426 Fit side-chains REVERT: L 72 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: M 86 LEU cc_start: 0.7869 (tt) cc_final: 0.7645 (mt) REVERT: H 81 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.4404 (mm-30) REVERT: H 159 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6244 (tp30) REVERT: E 14 ASP cc_start: 0.7037 (t0) cc_final: 0.6712 (t0) REVERT: F 3 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7474 (mptt) REVERT: F 30 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8286 (ttt) REVERT: I 1 MET cc_start: 0.1942 (tpt) cc_final: 0.1607 (mtm) REVERT: I 30 MET cc_start: 0.6815 (ttm) cc_final: 0.6554 (tpt) REVERT: N 29 TRP cc_start: 0.6888 (m100) cc_final: 0.6366 (m100) REVERT: S 25 PHE cc_start: 0.8014 (t80) cc_final: 0.7612 (t80) REVERT: W 26 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6741 (tp) REVERT: 0 15 GLU cc_start: 0.6793 (pm20) cc_final: 0.6407 (pm20) REVERT: m 241 ARG cc_start: 0.8534 (ttp-170) cc_final: 0.8304 (ttp-170) REVERT: h 135 LYS cc_start: 0.6637 (mmtp) cc_final: 0.6424 (mtpp) REVERT: h 160 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7480 (mp) REVERT: h 191 LEU cc_start: 0.8489 (mt) cc_final: 0.8218 (tp) REVERT: h 197 LYS cc_start: 0.8197 (tptp) cc_final: 0.7687 (tttt) REVERT: h 220 LYS cc_start: 0.7096 (ttpp) cc_final: 0.6633 (tptt) REVERT: h 228 LEU cc_start: 0.8203 (tp) cc_final: 0.7959 (tp) REVERT: h 231 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: k 1 MET cc_start: 0.6588 (tmm) cc_final: 0.5822 (tmm) REVERT: k 42 ASN cc_start: 0.8115 (t0) cc_final: 0.7843 (t0) REVERT: k 45 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6600 (mm-30) REVERT: o 47 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8125 (p) REVERT: q 9 MET cc_start: 0.6798 (mtm) cc_final: 0.6505 (mpp) REVERT: s 30 MET cc_start: 0.7700 (ttm) cc_final: 0.7480 (ttp) REVERT: u 45 GLU cc_start: 0.6423 (tt0) cc_final: 0.6118 (tp30) REVERT: y 30 MET cc_start: 0.4055 (ttt) cc_final: 0.3713 (ttp) REVERT: z 25 MET cc_start: 0.2561 (mtm) cc_final: 0.1758 (tmm) REVERT: ab 13 THR cc_start: 0.8282 (p) cc_final: 0.7988 (m) REVERT: ab 24 TYR cc_start: 0.8514 (t80) cc_final: 0.8314 (t80) REVERT: c 33 TRP cc_start: 0.8524 (m100) cc_final: 0.8321 (m100) outliers start: 74 outliers final: 51 residues processed: 593 average time/residue: 0.2377 time to fit residues: 238.8779 Evaluate side-chains 592 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 533 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 134 MET Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 229 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 247 LYS Chi-restraints excluded: chain a residue 45 GLU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain y residue 42 ASN Chi-restraints excluded: chain 5 residue 30 MET Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 3 residue 30 MET Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain ab residue 26 SER Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 69 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 404 optimal weight: 0.1980 chunk 136 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 335 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 323 optimal weight: 0.9990 chunk 336 optimal weight: 8.9990 chunk 327 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 GLN ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN h 35 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 GLN c 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.171054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.146840 restraints weight = 45513.265| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.36 r_work: 0.3107 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43866 Z= 0.137 Angle : 0.710 14.094 60339 Z= 0.279 Chirality : 0.037 0.213 5920 Planarity : 0.004 0.055 7401 Dihedral : 14.983 179.390 7332 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.06 % Allowed : 10.75 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.82 (0.12), residues: 4222 helix: 3.04 (0.09), residues: 2780 sheet: -0.98 (0.71), residues: 48 loop : -0.55 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 46 TYR 0.020 0.001 TYR A 41 PHE 0.017 0.001 PHE m 67 TRP 0.014 0.001 TRP Q 8 HIS 0.008 0.001 HIS j 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (43839) covalent geometry : angle 0.70964 / 0.28 (60339) hydrogen bonds : bond 0.05177 / 3.43 ( 2490) hydrogen bonds : angle 3.50204 / 2.49 ( 7074) Misc. bond : bond 0.00188 / 0.12 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 537 time to evaluate : 1.573 Fit side-chains REVERT: L 72 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7971 (pm20) REVERT: H 70 ARG cc_start: 0.7761 (mmt90) cc_final: 0.7328 (mmt90) REVERT: H 81 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.4210 (mm-30) REVERT: H 118 ARG cc_start: 0.7019 (ttp-110) cc_final: 0.6543 (ttm-80) REVERT: H 159 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6274 (tp30) REVERT: F 3 LYS cc_start: 0.7858 (mtpp) cc_final: 0.7322 (mptt) REVERT: F 30 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8287 (ttt) REVERT: I 30 MET cc_start: 0.6822 (ttm) cc_final: 0.6531 (tpt) REVERT: N 29 TRP cc_start: 0.6843 (m100) cc_final: 0.6291 (m100) REVERT: W 26 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6665 (tp) REVERT: 0 15 GLU cc_start: 0.6898 (pm20) cc_final: 0.6463 (pm20) REVERT: m 241 ARG cc_start: 0.8555 (ttp-170) cc_final: 0.8325 (ttp-170) REVERT: h 105 MET cc_start: 0.8085 (ttt) cc_final: 0.7712 (ttt) REVERT: h 160 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7457 (mp) REVERT: h 191 LEU cc_start: 0.8473 (mt) cc_final: 0.8138 (mt) REVERT: h 197 LYS cc_start: 0.8152 (tptp) cc_final: 0.7582 (tttt) REVERT: h 220 LYS cc_start: 0.7239 (ttpp) cc_final: 0.6668 (tptt) REVERT: h 228 LEU cc_start: 0.8147 (tp) cc_final: 0.7918 (tp) REVERT: h 231 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: j 25 MET cc_start: 0.7486 (mmt) cc_final: 0.7172 (mmm) REVERT: k 1 MET cc_start: 0.6437 (tmm) cc_final: 0.5698 (tmm) REVERT: o 47 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.8008 (p) REVERT: q 9 MET cc_start: 0.6949 (mtm) cc_final: 0.6567 (mpp) REVERT: s 9 MET cc_start: 0.5415 (mmp) cc_final: 0.5183 (mmp) REVERT: u 45 GLU cc_start: 0.6556 (tt0) cc_final: 0.6081 (tp30) REVERT: y 30 MET cc_start: 0.4145 (ttt) cc_final: 0.3814 (ttp) REVERT: z 25 MET cc_start: 0.2595 (mtm) cc_final: 0.1717 (tmm) REVERT: ab 13 THR cc_start: 0.8229 (p) cc_final: 0.8000 (m) REVERT: c 33 TRP cc_start: 0.8572 (m100) cc_final: 0.8362 (m100) outliers start: 75 outliers final: 53 residues processed: 582 average time/residue: 0.2300 time to fit residues: 226.8258 Evaluate side-chains 589 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 528 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 134 MET Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 202 ARG Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 229 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain a residue 45 GLU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain 5 residue 30 MET Chi-restraints excluded: chain 6 residue 2 SER Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 3 residue 30 MET Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain ab residue 26 SER Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 165 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 397 optimal weight: 5.9990 chunk 116 optimal weight: 0.0770 chunk 197 optimal weight: 0.0000 chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 381 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 overall best weight: 1.9546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.169274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.141800 restraints weight = 45540.543| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.48 r_work: 0.3169 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 43866 Z= 0.160 Angle : 0.749 19.664 60339 Z= 0.293 Chirality : 0.039 0.190 5920 Planarity : 0.005 0.055 7401 Dihedral : 15.080 179.381 7332 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.17 % Allowed : 11.21 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.71 (0.12), residues: 4222 helix: 2.93 (0.09), residues: 2780 sheet: -0.98 (0.71), residues: 48 loop : -0.54 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 46 TYR 0.022 0.001 TYR A 41 PHE 0.023 0.002 PHE o 25 TRP 0.014 0.001 TRP m 157 HIS 0.010 0.001 HIS m 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (43839) covalent geometry : angle 0.74857 / 0.29 (60339) hydrogen bonds : bond 0.05477 / 3.64 ( 2490) hydrogen bonds : angle 3.54004 / 2.52 ( 7074) Misc. bond : bond 0.00227 / 0.15 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 534 time to evaluate : 1.455 Fit side-chains REVERT: L 72 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: H 70 ARG cc_start: 0.7790 (mmt90) cc_final: 0.7436 (mmt90) REVERT: H 81 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.4499 (mm-30) REVERT: H 159 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6227 (tp30) REVERT: E 14 ASP cc_start: 0.7049 (t0) cc_final: 0.6812 (t70) REVERT: F 3 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7528 (mptt) REVERT: F 30 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8316 (ttt) REVERT: I 1 MET cc_start: 0.2313 (tpt) cc_final: 0.1982 (mtp) REVERT: I 30 MET cc_start: 0.6877 (ttm) cc_final: 0.6574 (tpt) REVERT: I 45 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6834 (mt-10) REVERT: W 26 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6720 (tp) REVERT: 0 15 GLU cc_start: 0.6796 (pm20) cc_final: 0.6486 (pm20) REVERT: m 241 ARG cc_start: 0.8552 (ttp-170) cc_final: 0.8295 (ttp-170) REVERT: h 105 MET cc_start: 0.8074 (ttt) cc_final: 0.7599 (ttt) REVERT: h 160 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7613 (mp) REVERT: h 191 LEU cc_start: 0.8487 (mt) cc_final: 0.8173 (mt) REVERT: h 197 LYS cc_start: 0.8219 (tptp) cc_final: 0.7854 (ttpt) REVERT: h 220 LYS cc_start: 0.7205 (ttpp) cc_final: 0.6827 (tmmt) REVERT: h 228 LEU cc_start: 0.8262 (tp) cc_final: 0.8011 (tp) REVERT: h 231 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: k 1 MET cc_start: 0.6696 (tmm) cc_final: 0.5926 (tmm) REVERT: o 47 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8140 (p) REVERT: q 9 MET cc_start: 0.6813 (mtm) cc_final: 0.6520 (mpp) REVERT: s 9 MET cc_start: 0.5520 (mmp) cc_final: 0.5287 (mmp) REVERT: u 45 GLU cc_start: 0.6427 (tt0) cc_final: 0.6107 (tp30) REVERT: y 30 MET cc_start: 0.4014 (ttt) cc_final: 0.3400 (ttm) REVERT: z 25 MET cc_start: 0.2226 (mtm) cc_final: 0.1638 (tmm) REVERT: ab 13 THR cc_start: 0.8254 (p) cc_final: 0.7984 (m) REVERT: c 17 THR cc_start: 0.8528 (m) cc_final: 0.8304 (m) REVERT: c 28 MET cc_start: 0.7660 (mmp) cc_final: 0.6905 (tmm) outliers start: 79 outliers final: 63 residues processed: 581 average time/residue: 0.2292 time to fit residues: 224.8882 Evaluate side-chains 597 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 526 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 134 MET Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 224 GLU Chi-restraints excluded: chain h residue 229 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain a residue 45 GLU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain t residue 40 LEU Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain y residue 42 ASN Chi-restraints excluded: chain 5 residue 30 MET Chi-restraints excluded: chain 6 residue 2 SER Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 3 residue 30 MET Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain ab residue 26 SER Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 268 optimal weight: 0.6980 chunk 296 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 344 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 GLN C 66 ASN h 35 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.167843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.140482 restraints weight = 45523.287| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.43 r_work: 0.3160 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 43866 Z= 0.177 Angle : 0.773 14.504 60339 Z= 0.305 Chirality : 0.039 0.219 5920 Planarity : 0.005 0.055 7401 Dihedral : 15.229 179.549 7332 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.06 % Allowed : 11.76 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.60 (0.12), residues: 4222 helix: 2.83 (0.09), residues: 2780 sheet: -1.02 (0.71), residues: 48 loop : -0.56 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 46 TYR 0.023 0.002 TYR A 41 PHE 0.024 0.002 PHE o 25 TRP 0.016 0.002 TRP Q 8 HIS 0.011 0.001 HIS m 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (43839) covalent geometry : angle 0.77335 / 0.30 (60339) hydrogen bonds : bond 0.05700 / 3.78 ( 2490) hydrogen bonds : angle 3.59579 / 2.56 ( 7074) Misc. bond : bond 0.00249 / 0.16 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 534 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: M 86 LEU cc_start: 0.7923 (tt) cc_final: 0.7617 (mt) REVERT: H 81 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.4567 (mm-30) REVERT: H 159 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6175 (tp30) REVERT: E 14 ASP cc_start: 0.7028 (t0) cc_final: 0.6806 (t70) REVERT: F 3 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7559 (mptt) REVERT: F 30 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8305 (ttt) REVERT: I 30 MET cc_start: 0.6871 (ttm) cc_final: 0.6573 (tpt) REVERT: I 45 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6756 (mt-10) REVERT: W 26 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6745 (tp) REVERT: 0 15 GLU cc_start: 0.6773 (pm20) cc_final: 0.6474 (pm20) REVERT: m 241 ARG cc_start: 0.8560 (ttp-170) cc_final: 0.8310 (ttp-170) REVERT: h 105 MET cc_start: 0.8105 (ttt) cc_final: 0.7607 (ttt) REVERT: h 160 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7661 (mp) REVERT: h 191 LEU cc_start: 0.8505 (mt) cc_final: 0.8198 (mt) REVERT: h 197 LYS cc_start: 0.8203 (tptp) cc_final: 0.7801 (tttt) REVERT: h 220 LYS cc_start: 0.7224 (ttpp) cc_final: 0.6860 (tmmt) REVERT: h 228 LEU cc_start: 0.8334 (tp) cc_final: 0.8065 (tp) REVERT: h 231 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8047 (m-30) REVERT: k 1 MET cc_start: 0.6770 (tmm) cc_final: 0.5947 (tmm) REVERT: o 47 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8113 (p) REVERT: q 9 MET cc_start: 0.6859 (mtm) cc_final: 0.6519 (mpp) REVERT: u 45 GLU cc_start: 0.6435 (tt0) cc_final: 0.6216 (tp30) REVERT: y 30 MET cc_start: 0.4102 (ttt) cc_final: 0.3808 (ttp) REVERT: z 25 MET cc_start: 0.2194 (mtm) cc_final: 0.1656 (tmm) REVERT: 3 45 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7982 (mt-10) REVERT: ab 13 THR cc_start: 0.8270 (p) cc_final: 0.7980 (m) REVERT: c 28 MET cc_start: 0.7700 (mmp) cc_final: 0.6847 (tmm) REVERT: c 33 TRP cc_start: 0.8591 (m100) cc_final: 0.8361 (m100) outliers start: 75 outliers final: 64 residues processed: 579 average time/residue: 0.2421 time to fit residues: 237.5020 Evaluate side-chains 593 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 521 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 134 MET Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 202 ARG Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 224 GLU Chi-restraints excluded: chain h residue 229 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain a residue 45 GLU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain t residue 40 LEU Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain y residue 42 ASN Chi-restraints excluded: chain 5 residue 30 MET Chi-restraints excluded: chain 6 residue 2 SER Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 3 residue 30 MET Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain ab residue 26 SER Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 11 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 123 optimal weight: 0.2980 chunk 320 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 GLN ** W 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.168818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.142665 restraints weight = 45701.044| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.35 r_work: 0.3186 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 43866 Z= 0.163 Angle : 0.752 15.078 60339 Z= 0.296 Chirality : 0.039 0.178 5920 Planarity : 0.005 0.055 7401 Dihedral : 15.125 179.637 7332 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.06 % Allowed : 11.85 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.64 (0.12), residues: 4222 helix: 2.86 (0.09), residues: 2780 sheet: -0.97 (0.71), residues: 48 loop : -0.54 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 46 TYR 0.022 0.002 TYR A 41 PHE 0.026 0.002 PHE o 25 TRP 0.016 0.002 TRP Q 8 HIS 0.010 0.001 HIS m 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (43839) covalent geometry : angle 0.75240 / 0.30 (60339) hydrogen bonds : bond 0.05556 / 3.69 ( 2490) hydrogen bonds : angle 3.57488 / 2.55 ( 7074) Misc. bond : bond 0.00227 / 0.14 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 529 time to evaluate : 1.550 Fit side-chains revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: M 86 LEU cc_start: 0.7949 (tt) cc_final: 0.7634 (mt) REVERT: H 81 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.4548 (mm-30) REVERT: H 159 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6190 (tp30) REVERT: E 14 ASP cc_start: 0.7011 (t0) cc_final: 0.6801 (t70) REVERT: F 3 LYS cc_start: 0.7866 (mtpp) cc_final: 0.7553 (mptt) REVERT: F 30 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8329 (ttt) REVERT: I 30 MET cc_start: 0.6857 (ttm) cc_final: 0.6587 (tpt) REVERT: T 12 LEU cc_start: 0.5870 (mp) cc_final: 0.5248 (pt) REVERT: W 26 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6737 (tp) REVERT: 0 15 GLU cc_start: 0.6749 (pm20) cc_final: 0.6456 (pm20) REVERT: m 241 ARG cc_start: 0.8548 (ttp-170) cc_final: 0.8298 (ttp-170) REVERT: h 105 MET cc_start: 0.8087 (ttt) cc_final: 0.7587 (ttt) REVERT: h 160 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7675 (mp) REVERT: h 191 LEU cc_start: 0.8514 (mt) cc_final: 0.8212 (mt) REVERT: h 197 LYS cc_start: 0.8203 (tptp) cc_final: 0.7813 (tttt) REVERT: h 220 LYS cc_start: 0.7211 (ttpp) cc_final: 0.6849 (tmmt) REVERT: h 228 LEU cc_start: 0.8325 (tp) cc_final: 0.8059 (tp) REVERT: h 231 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: k 1 MET cc_start: 0.6766 (tmm) cc_final: 0.5922 (tmm) REVERT: o 47 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.8126 (p) REVERT: q 9 MET cc_start: 0.6881 (mtm) cc_final: 0.6556 (mpp) REVERT: y 30 MET cc_start: 0.4093 (ttt) cc_final: 0.3752 (ttp) REVERT: z 25 MET cc_start: 0.2172 (mtm) cc_final: 0.1819 (tmm) REVERT: 3 45 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7997 (mt-10) REVERT: ab 13 THR cc_start: 0.8278 (p) cc_final: 0.8002 (m) REVERT: c 28 MET cc_start: 0.7825 (mmp) cc_final: 0.6914 (tmm) REVERT: c 33 TRP cc_start: 0.8578 (m100) cc_final: 0.8333 (m100) outliers start: 75 outliers final: 63 residues processed: 572 average time/residue: 0.2314 time to fit residues: 224.9242 Evaluate side-chains 595 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 524 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 33 THR Chi-restraints excluded: chain h residue 134 MET Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 160 ILE Chi-restraints excluded: chain h residue 200 SER Chi-restraints excluded: chain h residue 202 ARG Chi-restraints excluded: chain h residue 211 ASP Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 229 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain a residue 45 GLU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain t residue 40 LEU Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain y residue 42 ASN Chi-restraints excluded: chain 5 residue 30 MET Chi-restraints excluded: chain 6 residue 2 SER Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 3 residue 30 MET Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain ab residue 26 SER Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 229 optimal weight: 3.9990 chunk 323 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 394 optimal weight: 4.9990 chunk 372 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 309 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 347 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 GLN U 20 GLN ** W 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN h 35 ASN b 18 GLN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 42 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.163845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.129361 restraints weight = 46174.673| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.80 r_work: 0.3019 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 43866 Z= 0.206 Angle : 0.820 16.333 60339 Z= 0.325 Chirality : 0.041 0.184 5920 Planarity : 0.005 0.055 7401 Dihedral : 15.569 179.202 7332 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.06 % Allowed : 12.07 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 (0.12), residues: 4222 helix: 2.62 (0.09), residues: 2786 sheet: -1.12 (0.70), residues: 48 loop : -0.60 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG s 53 TYR 0.025 0.002 TYR A 41 PHE 0.028 0.002 PHE o 25 TRP 0.016 0.002 TRP Q 8 HIS 0.012 0.002 HIS m 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (43839) covalent geometry : angle 0.82030 / 0.33 (60339) hydrogen bonds : bond 0.06097 / 4.05 ( 2490) hydrogen bonds : angle 3.69730 / 2.64 ( 7074) Misc. bond : bond 0.00278 / 0.18 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10372.56 seconds wall clock time: 178 minutes 22.15 seconds (10702.15 seconds total)