Starting phenix.real_space_refine on Thu Dec 26 06:32:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7va9_31835/12_2024/7va9_31835.cif Found real_map, /net/cci-nas-00/data/ceres_data/7va9_31835/12_2024/7va9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7va9_31835/12_2024/7va9_31835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7va9_31835/12_2024/7va9_31835.map" model { file = "/net/cci-nas-00/data/ceres_data/7va9_31835/12_2024/7va9_31835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7va9_31835/12_2024/7va9_31835.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 1.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 40 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: 19 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-4': 1, 'SPO:plan-3': 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: 25.02, per 1000 atoms: 0.59 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: 13.30 Conformation dependent library (CDL) restraints added in 4.3 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: 3.36 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: 14.46 Time building geometry restraints manager: 14.15 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: 22402 35.93 - 71.86: 913 71.86 - 107.79: 87 107.79 - 143.72: 20 143.72 - 179.65: 9 Dihedral angle restraints: 23431 sinusoidal: 10811 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 23428 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 54 or resid 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 281 or resid 301 through 303)) selection = (chain 'l' and (resid 1 through 281 or resid 301 through 302 or (resid 303 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C1M or name C2 or name C \ 20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or na \ me C27 or name C28 or name 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 306 or resid 1301 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: 2.710 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: 0.040 Extract box with map and model: 1.570 Check model and map are aligned: 0.320 Set scattering table: 0.370 Process input model: 86.710 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.217 43839 Z= 1.054 Angle : 2.121 23.957 60339 Z= 0.780 Chirality : 0.049 0.452 5920 Planarity : 0.051 0.485 7401 Dihedral : 18.940 179.655 15295 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 15.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.062 0.003 TRP L 272 HIS 0.011 0.002 HIS p 39 PHE 0.080 0.003 PHE m 216 TYR 0.066 0.003 TYR H 236 ARG 0.021 0.002 ARG D 15 *********************** 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 : 3.894 Fit side-chains REVERT: H 232 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7565 (mtpp) 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: 0.6254 (tp) REVERT: C 61 GLN cc_start: 0.7258 (tp40) cc_final: 0.6793 (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: 0.4082 (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: 0.5445 time to fit residues: 670.6601 Evaluate side-chains 534 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 524 time to evaluate : 4.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain M residue 287 SER Chi-restraints excluded: chain H residue 232 LYS 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 342 optimal weight: 0.9980 chunk 307 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 chunk 318 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 368 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS ** C 66 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 aa 16 GLN ab 18 GLN ** c 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 43839 Z= 0.276 Angle : 0.872 15.565 60339 Z= 0.346 Chirality : 0.041 0.220 5920 Planarity : 0.006 0.057 7401 Dihedral : 17.698 179.845 7637 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.21 % Allowed : 6.02 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.12), residues: 4222 helix: 2.62 (0.09), residues: 2784 sheet: -1.53 (0.68), residues: 46 loop : -1.17 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 272 HIS 0.011 0.002 HIS x 39 PHE 0.047 0.002 PHE m 216 TYR 0.048 0.002 TYRaa 24 ARG 0.008 0.001 ARG j 46 *********************** 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 634 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 590 time to evaluate : 3.975 Fit side-chains revert: symmetry clash REVERT: H 175 MET cc_start: 0.7652 (ptm) cc_final: 0.7443 (ptm) REVERT: A 45 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6354 (mm-30) REVERT: B 46 ARG cc_start: 0.8750 (ttm-80) cc_final: 0.8545 (ttm170) REVERT: F 3 LYS cc_start: 0.7697 (mtpp) cc_final: 0.7310 (mptt) REVERT: I 3 LYS cc_start: 0.6420 (mttp) cc_final: 0.6067 (mttm) REVERT: J 40 LEU cc_start: 0.8439 (mt) cc_final: 0.8231 (mm) REVERT: W 26 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6736 (tp) REVERT: 7 6 LYS cc_start: 0.7882 (ptpt) cc_final: 0.7557 (mtpt) REVERT: 9 3 LYS cc_start: 0.7283 (ptpt) cc_final: 0.6991 (mttp) REVERT: C 27 MET cc_start: 0.8281 (mtt) cc_final: 0.7900 (mtt) REVERT: m 26 LEU cc_start: 0.8177 (mp) cc_final: 0.7904 (mp) REVERT: h 35 ASN cc_start: 0.8671 (m-40) cc_final: 0.8441 (m-40) REVERT: h 220 LYS cc_start: 0.7180 (ttpp) cc_final: 0.6750 (tmmt) REVERT: h 228 LEU cc_start: 0.7980 (tp) cc_final: 0.7731 (tp) REVERT: a 52 ASN cc_start: 0.7492 (OUTLIER) cc_final: 0.7287 (m-40) REVERT: i 1 MET cc_start: 0.3335 (tmm) cc_final: 0.2913 (tpp) REVERT: q 9 MET cc_start: 0.6416 (mtm) cc_final: 0.6138 (mpp) REVERT: z 25 MET cc_start: 0.2778 (mtm) cc_final: 0.1998 (tmm) REVERT: 3 20 GLN cc_start: 0.8593 (tt0) cc_final: 0.8306 (tt0) outliers start: 44 outliers final: 26 residues processed: 616 average time/residue: 0.5458 time to fit residues: 561.7776 Evaluate side-chains 580 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 551 time to evaluate : 4.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR 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 H residue 33 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain 9 residue 54 VAL Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 4 VAL 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 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 33 LEU 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 204 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 306 optimal weight: 0.9990 chunk 251 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 369 optimal weight: 6.9990 chunk 399 optimal weight: 0.9990 chunk 328 optimal weight: 2.9990 chunk 366 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 296 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 GLN ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 GLN ab 18 GLN ** c 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43839 Z= 0.172 Angle : 0.715 14.797 60339 Z= 0.280 Chirality : 0.037 0.208 5920 Planarity : 0.004 0.055 7401 Dihedral : 16.443 179.807 7620 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.13 % Allowed : 7.72 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.12), residues: 4222 helix: 3.01 (0.09), residues: 2772 sheet: -1.33 (0.70), residues: 46 loop : -0.90 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP l 272 HIS 0.008 0.001 HIS M 266 PHE 0.028 0.001 PHE k 23 TYR 0.022 0.001 TYR E 24 ARG 0.012 0.001 ARG J 46 *********************** 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 621 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 580 time to evaluate : 4.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: F 3 LYS cc_start: 0.7733 (mtpp) cc_final: 0.7366 (mptt) REVERT: I 1 MET cc_start: 0.1712 (tpt) cc_final: 0.1012 (tmm) REVERT: W 26 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6741 (tp) REVERT: 1 30 MET cc_start: 0.3361 (tmm) cc_final: 0.3075 (ptm) REVERT: l 59 TRP cc_start: 0.8207 (m100) cc_final: 0.7989 (m100) REVERT: m 234 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8219 (mt-10) REVERT: h 191 LEU cc_start: 0.8207 (mt) cc_final: 0.7905 (tp) REVERT: h 197 LYS cc_start: 0.7743 (tptt) cc_final: 0.7306 (ttpt) REVERT: h 220 LYS cc_start: 0.7113 (ttpp) cc_final: 0.6595 (tptt) REVERT: h 231 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: h 236 TYR cc_start: 0.8384 (t80) cc_final: 0.8148 (t80) REVERT: a 1 MET cc_start: 0.5809 (tpt) cc_final: 0.5267 (tpt) REVERT: d 46 ILE cc_start: 0.8657 (mt) cc_final: 0.8424 (mm) REVERT: i 1 MET cc_start: 0.3821 (tmm) cc_final: 0.3559 (tpp) REVERT: q 9 MET cc_start: 0.6375 (mtm) cc_final: 0.6121 (mpp) REVERT: u 23 PHE cc_start: 0.7865 (t80) cc_final: 0.7323 (t80) REVERT: u 45 GLU cc_start: 0.6179 (tt0) cc_final: 0.5786 (tp30) REVERT: z 25 MET cc_start: 0.2744 (mtm) cc_final: 0.1880 (tmm) REVERT: 3 20 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8203 (tt0) outliers start: 41 outliers final: 21 residues processed: 600 average time/residue: 0.5465 time to fit residues: 547.5722 Evaluate side-chains 571 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 546 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 GLU 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 181 VAL Chi-restraints excluded: chain H residue 218 THR 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 114 LEU 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 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 36 ILE Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain p residue 30 LEU Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain 6 residue 3 LYS Chi-restraints excluded: chain 3 residue 20 GLN Chi-restraints excluded: chain ab residue 26 SER 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 364 optimal weight: 5.9990 chunk 277 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 370 optimal weight: 10.0000 chunk 392 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 351 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 20 GLN 3 20 GLN ab 18 GLN c 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 43839 Z= 0.402 Angle : 0.907 15.945 60339 Z= 0.361 Chirality : 0.045 0.181 5920 Planarity : 0.006 0.116 7401 Dihedral : 16.941 179.740 7619 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.09 % Allowed : 8.77 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.12), residues: 4222 helix: 2.43 (0.09), residues: 2794 sheet: -1.41 (0.69), residues: 46 loop : -0.89 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 272 HIS 0.013 0.002 HIS m 182 PHE 0.026 0.003 PHE k 23 TYR 0.043 0.003 TYRab 24 ARG 0.010 0.001 ARGab 46 *********************** 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 637 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 561 time to evaluate : 4.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: H 81 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.4554 (mm-30) REVERT: B 19 GLU cc_start: 0.6887 (tt0) cc_final: 0.6638 (tt0) REVERT: E 14 ASP cc_start: 0.6706 (t0) cc_final: 0.6498 (t0) REVERT: F 3 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7408 (mptt) REVERT: N 29 TRP cc_start: 0.6749 (m100) cc_final: 0.6340 (m100) REVERT: S 25 PHE cc_start: 0.7923 (t80) cc_final: 0.7702 (t80) REVERT: W 26 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6841 (tp) REVERT: 1 30 MET cc_start: 0.3582 (tmm) cc_final: 0.3020 (ptm) REVERT: 0 15 GLU cc_start: 0.6679 (pm20) cc_final: 0.6285 (pm20) REVERT: m 233 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7680 (mtm-85) REVERT: h 160 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7632 (mp) REVERT: h 197 LYS cc_start: 0.8011 (tptt) cc_final: 0.7488 (tttt) REVERT: h 220 LYS cc_start: 0.7116 (ttpp) cc_final: 0.6736 (tmmt) REVERT: h 228 LEU cc_start: 0.8191 (tp) cc_final: 0.7906 (tp) REVERT: h 236 TYR cc_start: 0.8401 (t80) cc_final: 0.8145 (t80) REVERT: b 46 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7883 (mtt180) REVERT: o 47 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7927 (p) REVERT: q 9 MET cc_start: 0.6437 (mtm) cc_final: 0.6115 (mpp) REVERT: u 45 GLU cc_start: 0.6413 (tt0) cc_final: 0.6059 (tp30) REVERT: z 25 MET cc_start: 0.2552 (mtm) cc_final: 0.1871 (tmm) outliers start: 76 outliers final: 47 residues processed: 608 average time/residue: 0.6084 time to fit residues: 628.1305 Evaluate side-chains 585 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 532 time to evaluate : 4.035 ------------------------------------------------------------------------------- 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 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 E residue 16 GLN Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 9 residue 54 VAL 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 277 THR 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 211 ASP Chi-restraints excluded: chain h residue 221 SER 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 b residue 46 ARG 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 k residue 37 SER Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o 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 ab residue 26 SER Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 66 ASN 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 326 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 292 optimal weight: 0.0980 chunk 161 optimal weight: 2.9990 chunk 334 optimal weight: 0.8980 chunk 271 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 352 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 GLN ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN C 66 ASN h 35 ASN h 141 HIS ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN 3 20 GLN ab 18 GLN c 61 GLN c 66 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43839 Z= 0.185 Angle : 0.711 14.131 60339 Z= 0.279 Chirality : 0.037 0.192 5920 Planarity : 0.004 0.056 7401 Dihedral : 16.088 179.428 7619 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.70 % Allowed : 10.20 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.12), residues: 4222 helix: 2.91 (0.09), residues: 2778 sheet: -1.12 (0.71), residues: 46 loop : -0.67 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP l 271 HIS 0.007 0.001 HIS M 266 PHE 0.026 0.001 PHE k 23 TYR 0.017 0.001 TYR G 24 ARG 0.005 0.000 ARG g 46 *********************** 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 629 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 567 time to evaluate : 4.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: H 70 ARG cc_start: 0.7644 (mmt90) cc_final: 0.7379 (mmt90) REVERT: F 3 LYS cc_start: 0.7771 (mtpp) cc_final: 0.7410 (mptt) REVERT: N 29 TRP cc_start: 0.6737 (m100) cc_final: 0.6229 (m100) REVERT: S 25 PHE cc_start: 0.7818 (t80) cc_final: 0.7559 (t80) REVERT: W 26 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6817 (tp) REVERT: 0 15 GLU cc_start: 0.6626 (pm20) cc_final: 0.6220 (pm20) REVERT: C 6 ILE cc_start: 0.4180 (OUTLIER) cc_final: 0.3931 (tp) REVERT: m 4 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8327 (mm-40) REVERT: m 234 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8184 (mt-10) REVERT: m 241 ARG cc_start: 0.8375 (ttp-170) cc_final: 0.8160 (ttp-170) REVERT: h 191 LEU cc_start: 0.8424 (mt) cc_final: 0.8043 (mt) REVERT: h 197 LYS cc_start: 0.7954 (tptt) cc_final: 0.7476 (tttt) REVERT: h 220 LYS cc_start: 0.7112 (ttpp) cc_final: 0.6723 (tmmt) REVERT: h 228 LEU cc_start: 0.7991 (tp) cc_final: 0.7732 (tp) REVERT: h 231 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: h 236 TYR cc_start: 0.8400 (t80) cc_final: 0.8119 (t80) REVERT: k 1 MET cc_start: 0.6144 (tmm) cc_final: 0.5388 (tmm) REVERT: k 37 SER cc_start: 0.8250 (OUTLIER) cc_final: 0.7980 (m) REVERT: k 42 ASN cc_start: 0.7978 (t0) cc_final: 0.7717 (t0) REVERT: k 45 GLU cc_start: 0.6230 (mm-30) cc_final: 0.5977 (mm-30) REVERT: o 47 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7955 (p) REVERT: q 9 MET cc_start: 0.6477 (mtm) cc_final: 0.6250 (mpp) REVERT: s 9 MET cc_start: 0.5024 (mmp) cc_final: 0.4708 (mmp) REVERT: u 23 PHE cc_start: 0.7782 (t80) cc_final: 0.7345 (t80) REVERT: u 45 GLU cc_start: 0.6296 (tt0) cc_final: 0.6008 (tp30) REVERT: z 25 MET cc_start: 0.2447 (mtm) cc_final: 0.1760 (tmm) outliers start: 62 outliers final: 40 residues processed: 600 average time/residue: 0.5287 time to fit residues: 529.6701 Evaluate side-chains 590 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 544 time to evaluate : 4.097 ------------------------------------------------------------------------------- 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 138 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 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 B residue 14 ASP Chi-restraints excluded: chain N residue 28 LEU 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 C residue 6 ILE Chi-restraints excluded: chain C residue 66 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 202 ARG Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 247 LYS Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain k residue 37 SER 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 u residue 52 ASN Chi-restraints excluded: chain w residue 26 LEU 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 26 SER Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 66 ASN 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 132 optimal weight: 0.8980 chunk 353 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 230 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 392 optimal weight: 3.9990 chunk 326 optimal weight: 0.0980 chunk 181 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 GLN c 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 43839 Z= 0.150 Angle : 0.663 13.875 60339 Z= 0.259 Chirality : 0.035 0.168 5920 Planarity : 0.004 0.054 7401 Dihedral : 15.463 179.401 7619 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.57 % Allowed : 10.83 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.12), residues: 4222 helix: 3.21 (0.09), residues: 2768 sheet: -0.97 (0.72), residues: 48 loop : -0.52 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP l 271 HIS 0.006 0.001 HIS M 266 PHE 0.021 0.001 PHE k 23 TYR 0.017 0.001 TYR P 24 ARG 0.004 0.000 ARG s 53 *********************** 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 632 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 575 time to evaluate : 4.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: H 70 ARG cc_start: 0.7638 (mmt90) cc_final: 0.7386 (mmt90) REVERT: H 81 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.4148 (mm-30) REVERT: H 103 ASP cc_start: 0.7778 (t70) cc_final: 0.7351 (t0) REVERT: H 159 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6164 (tp30) REVERT: F 3 LYS cc_start: 0.7730 (mtpp) cc_final: 0.7390 (mptt) REVERT: N 29 TRP cc_start: 0.6670 (m100) cc_final: 0.6072 (m100) REVERT: S 25 PHE cc_start: 0.7718 (t80) cc_final: 0.7335 (t80) REVERT: W 26 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6632 (tp) REVERT: 0 15 GLU cc_start: 0.6634 (pm20) cc_final: 0.6212 (pm20) REVERT: l 59 TRP cc_start: 0.8200 (m100) cc_final: 0.7976 (m100) REVERT: m 4 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8283 (mm-40) REVERT: m 234 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8084 (mt-10) REVERT: m 241 ARG cc_start: 0.8343 (ttp-170) cc_final: 0.8082 (ttp-170) REVERT: h 191 LEU cc_start: 0.8333 (mt) cc_final: 0.8012 (mt) REVERT: h 197 LYS cc_start: 0.7979 (tptt) cc_final: 0.7522 (tttt) REVERT: h 220 LYS cc_start: 0.7043 (ttpp) cc_final: 0.6687 (tmmt) REVERT: h 228 LEU cc_start: 0.7853 (tp) cc_final: 0.7566 (tp) REVERT: h 231 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: h 236 TYR cc_start: 0.8306 (t80) cc_final: 0.7998 (t80) REVERT: k 1 MET cc_start: 0.6174 (tmm) cc_final: 0.5305 (tmm) REVERT: k 30 MET cc_start: 0.7299 (ttt) cc_final: 0.6993 (ttm) REVERT: o 47 SER cc_start: 0.8170 (t) cc_final: 0.7963 (p) REVERT: q 9 MET cc_start: 0.6486 (mtm) cc_final: 0.6285 (mpp) REVERT: s 41 TYR cc_start: 0.6614 (m-80) cc_final: 0.6273 (m-80) REVERT: u 23 PHE cc_start: 0.7787 (t80) cc_final: 0.7333 (t80) REVERT: u 45 GLU cc_start: 0.6394 (tt0) cc_final: 0.5978 (tp30) REVERT: z 25 MET cc_start: 0.2280 (mtm) cc_final: 0.1710 (tmm) outliers start: 57 outliers final: 44 residues processed: 603 average time/residue: 0.5406 time to fit residues: 549.7080 Evaluate side-chains 594 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 545 time to evaluate : 4.170 ------------------------------------------------------------------------------- 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 138 MET 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 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 B residue 14 ASP Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l 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 143 SER 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 b residue 26 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain w residue 26 LEU 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 66 ASN 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 378 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 286 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 330 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 chunk 391 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 HIS ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN a 20 GLN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 GLN c 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43839 Z= 0.203 Angle : 0.708 14.135 60339 Z= 0.278 Chirality : 0.037 0.156 5920 Planarity : 0.004 0.055 7401 Dihedral : 15.516 179.459 7619 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.79 % Allowed : 11.43 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.12), residues: 4222 helix: 3.09 (0.09), residues: 2780 sheet: -0.98 (0.72), residues: 48 loop : -0.49 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 252 HIS 0.010 0.001 HIS m 182 PHE 0.020 0.001 PHE k 23 TYR 0.020 0.001 TYR F 41 ARG 0.004 0.000 ARG s 53 *********************** 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 616 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 551 time to evaluate : 3.856 Fit side-chains revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: H 70 ARG cc_start: 0.7658 (mmt90) cc_final: 0.7402 (mmt90) REVERT: H 81 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.4264 (mm-30) REVERT: H 159 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6086 (tp30) REVERT: F 3 LYS cc_start: 0.7740 (mtpp) cc_final: 0.7403 (mptt) REVERT: I 45 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6369 (mt-10) REVERT: N 29 TRP cc_start: 0.6638 (m100) cc_final: 0.6056 (m100) REVERT: S 25 PHE cc_start: 0.7850 (t80) cc_final: 0.7481 (t80) REVERT: W 26 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6648 (tp) REVERT: W 41 TYR cc_start: 0.6382 (m-80) cc_final: 0.6088 (m-80) REVERT: 0 15 GLU cc_start: 0.6676 (pm20) cc_final: 0.6294 (pm20) REVERT: l 59 TRP cc_start: 0.8222 (m100) cc_final: 0.7956 (m100) REVERT: m 4 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8317 (mm110) REVERT: m 241 ARG cc_start: 0.8364 (ttp-170) cc_final: 0.8105 (ttp-170) REVERT: h 160 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7257 (mp) REVERT: h 191 LEU cc_start: 0.8391 (mt) cc_final: 0.8079 (mt) REVERT: h 197 LYS cc_start: 0.7972 (tptp) cc_final: 0.7531 (tttt) REVERT: h 220 LYS cc_start: 0.7033 (ttpp) cc_final: 0.6670 (tmmt) REVERT: h 228 LEU cc_start: 0.7951 (tp) cc_final: 0.7696 (tp) REVERT: h 231 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: k 1 MET cc_start: 0.6368 (tmm) cc_final: 0.5475 (tmm) REVERT: o 47 SER cc_start: 0.8174 (OUTLIER) cc_final: 0.7967 (p) REVERT: q 9 MET cc_start: 0.6452 (mtm) cc_final: 0.6222 (mpp) REVERT: u 23 PHE cc_start: 0.7708 (t80) cc_final: 0.7281 (t80) REVERT: u 45 GLU cc_start: 0.6274 (tt0) cc_final: 0.5961 (tp30) REVERT: u 52 ASN cc_start: 0.6042 (t0) cc_final: 0.5617 (t0) REVERT: x 25 MET cc_start: 0.4668 (tpp) cc_final: 0.4122 (tpp) REVERT: z 25 MET cc_start: 0.2229 (mtm) cc_final: 0.1676 (tmm) REVERT: c 58 GLN cc_start: 0.7429 (tp-100) cc_final: 0.7100 (tp40) outliers start: 65 outliers final: 49 residues processed: 583 average time/residue: 0.5234 time to fit residues: 515.0076 Evaluate side-chains 595 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 539 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 72 GLU 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 B residue 14 ASP Chi-restraints excluded: chain F residue 10 ILE 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 C residue 60 ASN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l 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 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 a residue 45 GLU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain k residue 37 SER 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 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 42 LEU Chi-restraints excluded: chain c residue 66 ASN 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 242 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 233 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 248 optimal weight: 0.0980 chunk 266 optimal weight: 7.9990 chunk 193 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN E 18 GLN R 21 HIS C 66 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 GLN c 66 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43839 Z= 0.153 Angle : 0.664 13.866 60339 Z= 0.260 Chirality : 0.036 0.170 5920 Planarity : 0.004 0.054 7401 Dihedral : 15.241 179.737 7619 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.70 % Allowed : 11.85 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.12), residues: 4222 helix: 3.23 (0.09), residues: 2780 sheet: -0.83 (0.74), residues: 48 loop : -0.42 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 157 HIS 0.006 0.001 HIS M 266 PHE 0.018 0.001 PHE k 23 TYR 0.019 0.001 TYR P 24 ARG 0.003 0.000 ARG s 53 *********************** 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 604 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 542 time to evaluate : 4.083 Fit side-chains REVERT: L 72 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: H 70 ARG cc_start: 0.7634 (mmt90) cc_final: 0.7379 (mmt90) REVERT: H 81 GLU cc_start: 0.5861 (OUTLIER) cc_final: 0.4224 (mm-30) REVERT: H 159 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6105 (tp30) REVERT: F 3 LYS cc_start: 0.7717 (mtpp) cc_final: 0.7401 (mptt) REVERT: I 45 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6376 (mt-10) REVERT: O 25 PHE cc_start: 0.8871 (t80) cc_final: 0.8576 (t80) REVERT: S 25 PHE cc_start: 0.7795 (t80) cc_final: 0.7447 (t80) REVERT: W 26 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6660 (tp) REVERT: 1 30 MET cc_start: 0.3340 (tmm) cc_final: 0.2765 (ppp) REVERT: 0 15 GLU cc_start: 0.6644 (pm20) cc_final: 0.6277 (pm20) REVERT: l 59 TRP cc_start: 0.8185 (m100) cc_final: 0.7962 (m100) REVERT: m 4 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8297 (mm110) REVERT: m 234 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8165 (mt-10) REVERT: m 241 ARG cc_start: 0.8334 (ttp-170) cc_final: 0.8052 (ttp-170) REVERT: h 191 LEU cc_start: 0.8377 (mt) cc_final: 0.8081 (mt) REVERT: h 197 LYS cc_start: 0.7963 (tptp) cc_final: 0.7526 (tttt) REVERT: h 220 LYS cc_start: 0.7001 (ttpp) cc_final: 0.6609 (tptt) REVERT: h 228 LEU cc_start: 0.7852 (tp) cc_final: 0.7558 (tp) REVERT: k 1 MET cc_start: 0.6383 (tmm) cc_final: 0.5453 (tmm) REVERT: k 30 MET cc_start: 0.7319 (ttt) cc_final: 0.6994 (ttm) REVERT: q 9 MET cc_start: 0.6538 (mtm) cc_final: 0.6283 (mpp) REVERT: s 8 TRP cc_start: 0.5329 (m100) cc_final: 0.4831 (m100) REVERT: u 45 GLU cc_start: 0.6370 (tt0) cc_final: 0.6059 (tp30) REVERT: u 52 ASN cc_start: 0.6043 (t0) cc_final: 0.5653 (t0) REVERT: x 25 MET cc_start: 0.4615 (tpp) cc_final: 0.4123 (tpp) REVERT: z 25 MET cc_start: 0.2006 (mtm) cc_final: 0.1575 (tmm) REVERT: c 58 GLN cc_start: 0.7365 (tp-100) cc_final: 0.7055 (tp40) outliers start: 62 outliers final: 48 residues processed: 574 average time/residue: 0.5902 time to fit residues: 577.4893 Evaluate side-chains 581 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 529 time to evaluate : 4.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 138 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 218 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain G residue 40 LEU 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 C residue 60 ASN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 216 PHE 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 143 SER 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 a residue 45 GLU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain w residue 26 LEU 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 66 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 355 optimal weight: 6.9990 chunk 374 optimal weight: 5.9990 chunk 342 optimal weight: 4.9990 chunk 364 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 329 optimal weight: 1.9990 chunk 344 optimal weight: 2.9990 chunk 363 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 21 HIS C 66 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 GLN c 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43839 Z= 0.270 Angle : 0.773 14.225 60339 Z= 0.306 Chirality : 0.040 0.167 5920 Planarity : 0.005 0.055 7401 Dihedral : 15.718 179.458 7619 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.68 % Allowed : 12.31 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.12), residues: 4222 helix: 2.92 (0.09), residues: 2780 sheet: -0.97 (0.71), residues: 48 loop : -0.49 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 252 HIS 0.012 0.001 HIS m 182 PHE 0.020 0.002 PHE k 23 TYR 0.022 0.002 TYR F 41 ARG 0.006 0.001 ARG k 53 *********************** 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 596 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 535 time to evaluate : 4.084 Fit side-chains REVERT: L 72 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: H 70 ARG cc_start: 0.7616 (mmt90) cc_final: 0.7328 (mmt90) REVERT: H 81 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.4443 (mm-30) REVERT: H 159 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6012 (tp30) REVERT: F 3 LYS cc_start: 0.7805 (mtpp) cc_final: 0.7451 (mptt) REVERT: I 45 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6363 (mt-10) REVERT: S 25 PHE cc_start: 0.7936 (t80) cc_final: 0.7714 (t80) REVERT: W 26 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6706 (tp) REVERT: W 41 TYR cc_start: 0.6475 (m-80) cc_final: 0.6225 (m-80) REVERT: 1 30 MET cc_start: 0.3249 (tmm) cc_final: 0.2838 (ppp) REVERT: 0 15 GLU cc_start: 0.6651 (pm20) cc_final: 0.6350 (pm20) REVERT: l 202 LYS cc_start: 0.7296 (tmmt) cc_final: 0.6779 (tmmt) REVERT: m 4 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8328 (mm110) REVERT: m 241 ARG cc_start: 0.8425 (ttp-170) cc_final: 0.8175 (ttp-170) REVERT: h 160 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7472 (mp) REVERT: h 191 LEU cc_start: 0.8510 (mt) cc_final: 0.8206 (mt) REVERT: h 197 LYS cc_start: 0.7983 (tptp) cc_final: 0.7620 (tttt) REVERT: h 220 LYS cc_start: 0.7073 (ttpp) cc_final: 0.6716 (tmmt) REVERT: h 228 LEU cc_start: 0.8084 (tp) cc_final: 0.7838 (tp) REVERT: k 1 MET cc_start: 0.6443 (tmm) cc_final: 0.5427 (tmm) REVERT: q 9 MET cc_start: 0.6527 (mtm) cc_final: 0.6238 (mpp) REVERT: u 45 GLU cc_start: 0.6319 (tt0) cc_final: 0.6103 (tp30) REVERT: u 52 ASN cc_start: 0.6069 (t0) cc_final: 0.5702 (t0) REVERT: x 25 MET cc_start: 0.4720 (tpp) cc_final: 0.4094 (tpp) REVERT: z 25 MET cc_start: 0.1992 (mtm) cc_final: 0.1652 (tmm) REVERT: c 17 THR cc_start: 0.8363 (m) cc_final: 0.8153 (m) REVERT: c 58 GLN cc_start: 0.7423 (tp-100) cc_final: 0.7133 (tp-100) outliers start: 61 outliers final: 47 residues processed: 570 average time/residue: 0.5307 time to fit residues: 508.9776 Evaluate side-chains 572 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 520 time to evaluate : 4.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 138 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 296 VAL 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 B residue 14 ASP 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 C residue 60 ASN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 1 MET 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 221 SER Chi-restraints excluded: chain h residue 229 GLU Chi-restraints excluded: chain a residue 45 GLU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE 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 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 239 optimal weight: 0.9990 chunk 385 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 404 optimal weight: 5.9990 chunk 372 optimal weight: 0.3980 chunk 322 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 248 optimal weight: 0.9980 chunk 197 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN C 66 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 GLN c 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43839 Z= 0.253 Angle : 0.757 14.537 60339 Z= 0.299 Chirality : 0.039 0.162 5920 Planarity : 0.005 0.055 7401 Dihedral : 15.696 179.349 7619 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.62 % Allowed : 12.62 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.12), residues: 4222 helix: 2.85 (0.09), residues: 2780 sheet: -1.01 (0.72), residues: 48 loop : -0.51 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Q 8 HIS 0.010 0.001 HIS m 182 PHE 0.022 0.002 PHE k 23 TYR 0.022 0.002 TYR F 41 ARG 0.006 0.001 ARG k 53 ********************** 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 588 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 529 time to evaluate : 4.058 Fit side-chains REVERT: L 72 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: H 70 ARG cc_start: 0.7622 (mmt90) cc_final: 0.7325 (mmt90) REVERT: H 81 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.4453 (mm-30) REVERT: H 159 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.5987 (tp30) REVERT: F 3 LYS cc_start: 0.7794 (mtpp) cc_final: 0.7468 (mptt) REVERT: I 45 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6406 (mt-10) REVERT: S 25 PHE cc_start: 0.7939 (t80) cc_final: 0.7737 (t80) REVERT: W 26 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6707 (tp) REVERT: W 41 TYR cc_start: 0.6481 (m-80) cc_final: 0.6219 (m-80) REVERT: 1 30 MET cc_start: 0.3257 (tmm) cc_final: 0.2848 (ptm) REVERT: 0 15 GLU cc_start: 0.6623 (pm20) cc_final: 0.6313 (pm20) REVERT: m 4 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8312 (mm110) REVERT: m 241 ARG cc_start: 0.8411 (ttp-170) cc_final: 0.8164 (ttp-170) REVERT: h 160 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7492 (mp) REVERT: h 191 LEU cc_start: 0.8503 (mt) cc_final: 0.8204 (mt) REVERT: h 197 LYS cc_start: 0.7977 (tptp) cc_final: 0.7614 (tttt) REVERT: h 228 LEU cc_start: 0.8091 (tp) cc_final: 0.7844 (tp) REVERT: k 1 MET cc_start: 0.6475 (tmm) cc_final: 0.5428 (tmm) REVERT: q 9 MET cc_start: 0.6560 (mtm) cc_final: 0.6273 (mpp) REVERT: s 8 TRP cc_start: 0.5440 (m100) cc_final: 0.4812 (m100) REVERT: z 25 MET cc_start: 0.1970 (mtm) cc_final: 0.1686 (tmm) REVERT: c 17 THR cc_start: 0.8381 (m) cc_final: 0.8163 (m) REVERT: c 58 GLN cc_start: 0.7477 (tp-100) cc_final: 0.7152 (tp-100) outliers start: 59 outliers final: 49 residues processed: 563 average time/residue: 0.5546 time to fit residues: 527.2253 Evaluate side-chains 577 residues out of total 3638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 523 time to evaluate : 4.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 138 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 296 VAL 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 B residue 14 ASP 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 9 residue 54 VAL Chi-restraints excluded: chain C residue 60 ASN 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 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 a residue 45 GLU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain j residue 44 ILE Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE 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 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 255 optimal weight: 7.9990 chunk 343 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 296 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 322 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 331 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 20 GLN C 66 ASN ** j 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 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 = 0.3787 r_free = 0.3787 target = 0.170889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.147993 restraints weight = 45574.391| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.28 r_work: 0.3251 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43839 Z= 0.187 Angle : 0.707 16.515 60339 Z= 0.278 Chirality : 0.037 0.158 5920 Planarity : 0.004 0.055 7401 Dihedral : 15.393 179.539 7619 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.51 % Allowed : 12.89 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.12), residues: 4222 helix: 3.02 (0.09), residues: 2780 sheet: -0.89 (0.73), residues: 48 loop : -0.46 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 8 HIS 0.008 0.001 HIS m 182 PHE 0.019 0.001 PHE m 67 TYR 0.021 0.001 TYR P 24 ARG 0.006 0.000 ARG k 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9645.83 seconds wall clock time: 177 minutes 32.61 seconds (10652.61 seconds total)