Starting phenix.real_space_refine on Sat Mar 7 03:52:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vb9_31875/03_2026/7vb9_31875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vb9_31875/03_2026/7vb9_31875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vb9_31875/03_2026/7vb9_31875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vb9_31875/03_2026/7vb9_31875.map" model { file = "/net/cci-nas-00/data/ceres_data/7vb9_31875/03_2026/7vb9_31875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vb9_31875/03_2026/7vb9_31875.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 11 5.49 5 Mg 51 5.21 5 S 143 5.16 5 C 25539 2.51 5 N 5208 2.21 5 O 5520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36474 Number of models: 1 Model: "" Number of chains: 100 Chain: "L" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2132 Classifications: {'peptide': 268} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 254} 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: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "N" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "O" 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: "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: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 500 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} 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: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 320 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} 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: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} 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: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "u" 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: "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: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "y" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "z" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 312 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain breaks: 1 Chain: "5" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "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: "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: "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: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 529 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "L" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 336 Unusual residues: {'BCL': 3, 'BPH': 2, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1, 'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 19 Chain: "M" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {'BCL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'BCL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 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: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 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: "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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "J" 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: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" 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: "8" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "9" 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: "0" 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: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 157 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "l" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 312 Unusual residues: {'BCL': 2, 'BPH': 2, 'U10': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 319 Unusual residues: {'BCL': 2, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "a" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 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: 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: "e" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 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: 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: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "j" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 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: 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: "q" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "r" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "s" 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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "v" 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: "w" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} 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: 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: "4" 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: "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: "Q" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} 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: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.07, per 1000 atoms: 0.25 Number of scatterers: 36474 At special positions: 0 Unit cell: (217.895, 130.903, 121.789, 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 143 16.00 P 11 15.00 Mg 51 11.99 O 5520 8.00 N 5208 7.00 C 25539 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=23, symmetry=0 Number of additional bonds: simple=23, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 1.3 seconds 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7064 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 12 sheets defined 71.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 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 85 through 112 removed outlier: 3.581A pdb=" N ILE L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.587A pdb=" N PHE L 119 " --> pdb=" O TYR L 115 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 removed outlier: 3.559A pdb=" N VAL L 137 " --> pdb=" O LEU L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.755A pdb=" N TYR L 144 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 164 Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 Processing helix chain 'L' and resid 227 through 250 Processing helix chain 'L' and resid 258 through 268 removed outlier: 4.185A pdb=" N TRP L 262 " --> pdb=" O GLN L 258 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 41 Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 112 through 141 removed outlier: 3.513A 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: 3.620A 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: 3.610A pdb=" N GLU M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 287 removed outlier: 3.614A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'H' and resid 11 through 36 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 removed outlier: 3.632A pdb=" N ALA H 112 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 137 No H-bonds generated for 'chain 'H' and resid 135 through 137' Processing helix chain 'H' and resid 209 through 216 removed outlier: 4.102A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE H 216 " --> pdb=" O PHE H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 removed outlier: 3.963A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.406A 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 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'B' and resid 13 through 46 Processing helix chain 'D' and resid 1 through 10 removed outlier: 3.631A pdb=" N PHE D 4 " --> pdb=" O MET D 1 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 38 removed outlier: 3.574A 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 1 through 10 removed outlier: 3.632A pdb=" N PHE F 4 " --> pdb=" O MET F 1 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR F 5 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 38 removed outlier: 3.574A 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 1 through 10 removed outlier: 3.631A pdb=" N PHE I 4 " --> pdb=" O MET I 1 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR I 5 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 38 removed outlier: 3.573A 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 12 through 38 removed outlier: 3.763A pdb=" N VAL K 16 " --> pdb=" O ASP K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'N' and resid 13 through 46 Processing helix chain 'O' and resid 13 through 38 Processing helix chain 'O' and resid 42 through 51 Processing helix chain '7' and resid 1 through 10 removed outlier: 3.630A pdb=" N PHE 7 4 " --> pdb=" O MET 7 1 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR 7 5 " --> pdb=" O SER 7 2 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 38 removed outlier: 3.574A 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 1 through 10 removed outlier: 3.632A pdb=" N PHE 9 4 " --> pdb=" O MET 9 1 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR 9 5 " --> pdb=" O SER 9 2 " (cutoff:3.500A) Processing helix chain '9' and resid 12 through 38 removed outlier: 3.574A pdb=" N THR 9 38 " --> pdb=" O ILE 9 34 " (cutoff:3.500A) Processing helix chain '9' and resid 42 through 52 Processing helix chain '0' and resid 13 through 46 Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 14 through 55 removed outlier: 4.028A pdb=" N ALA C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 10 removed outlier: 3.882A pdb=" N LYS l 8 " --> pdb=" O PHE l 5 " (cutoff:3.500A) 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: 3.607A pdb=" N PHE l 119 " --> pdb=" O TYR l 115 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE l 123 " --> pdb=" O PHE l 119 " (cutoff:3.500A) removed outlier: 3.857A 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: 3.714A pdb=" N TYR l 144 " --> pdb=" O ALA l 141 " (cutoff:3.500A) Processing helix chain 'l' and resid 152 through 163 Processing helix chain 'l' and resid 170 through 199 removed outlier: 3.582A pdb=" N ALA l 176 " --> pdb=" O ALA l 172 " (cutoff:3.500A) Processing helix chain 'l' and resid 208 through 221 Processing helix chain 'l' and resid 225 through 250 Processing helix chain 'l' and resid 259 through 268 removed outlier: 3.822A pdb=" N TRP l 263 " --> pdb=" O TRP l 259 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP l 265 " --> pdb=" O ASP l 261 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP l 266 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 41 Processing helix chain 'm' and resid 53 through 78 Processing helix chain 'm' and resid 81 through 88 Processing helix chain 'm' and resid 98 through 102 Processing helix chain 'm' and resid 112 through 141 removed outlier: 3.510A 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: 3.621A 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: 3.609A pdb=" N GLU m 246 " --> pdb=" O GLY m 242 " (cutoff:3.500A) Processing helix chain 'm' and resid 263 through 287 removed outlier: 3.615A pdb=" N ARG m 267 " --> pdb=" O GLU m 263 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 293 through 301 Processing helix chain 'h' and resid 11 through 36 Processing helix chain 'h' and resid 103 through 108 Processing helix chain 'h' and resid 109 through 113 removed outlier: 3.632A pdb=" N ALA h 112 " --> pdb=" O VAL h 109 " (cutoff:3.500A) Processing helix chain 'h' and resid 135 through 137 No H-bonds generated for 'chain 'h' and resid 135 through 137' Processing helix chain 'h' and resid 209 through 216 removed outlier: 4.101A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE h 216 " --> pdb=" O PHE h 213 " (cutoff:3.500A) Processing helix chain 'h' and resid 226 through 244 removed outlier: 3.963A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.405A 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 Processing helix chain 'a' and resid 42 through 51 Processing helix chain 'b' and resid 13 through 46 Processing helix chain 'd' and resid 1 through 10 removed outlier: 3.630A pdb=" N PHE d 4 " --> pdb=" O MET d 1 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 38 removed outlier: 3.573A 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 1 through 10 removed outlier: 3.631A pdb=" N PHE f 4 " --> pdb=" O MET f 1 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR f 5 " --> pdb=" O SER f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 38 removed outlier: 3.573A 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 1 through 10 removed outlier: 3.630A pdb=" N PHE i 4 " --> pdb=" O MET i 1 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR i 5 " --> pdb=" O SER i 2 " (cutoff:3.500A) Processing helix chain 'i' and resid 12 through 38 removed outlier: 3.573A 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 1 through 10 removed outlier: 3.632A pdb=" N PHE k 4 " --> pdb=" O MET k 1 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR k 5 " --> pdb=" O SER k 2 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 38 removed outlier: 3.573A 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 13 through 46 Processing helix chain 'o' and resid 1 through 10 removed outlier: 3.630A pdb=" N PHE o 4 " --> pdb=" O MET o 1 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR o 5 " --> pdb=" O SER o 2 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 38 removed outlier: 3.573A pdb=" N THR o 38 " --> pdb=" O ILE o 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 51 Processing helix chain 'p' and resid 13 through 46 Processing helix chain 'q' and resid 1 through 10 removed outlier: 3.631A pdb=" N PHE q 4 " --> pdb=" O MET q 1 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR q 5 " --> pdb=" O SER q 2 " (cutoff:3.500A) Processing helix chain 'q' and resid 12 through 38 removed outlier: 3.573A 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 13 through 46 Processing helix chain 's' and resid 1 through 10 removed outlier: 3.631A pdb=" N PHE s 4 " --> pdb=" O MET s 1 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR s 5 " --> pdb=" O SER s 2 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 38 removed outlier: 3.574A pdb=" N THR s 38 " --> pdb=" O ILE s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 51 Processing helix chain 't' and resid 13 through 46 Processing helix chain 'u' and resid 1 through 10 removed outlier: 3.631A pdb=" N PHE u 4 " --> pdb=" O MET u 1 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR u 5 " --> pdb=" O SER u 2 " (cutoff:3.500A) Processing helix chain 'u' and resid 12 through 38 removed outlier: 3.573A 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 Processing helix chain 'w' and resid 42 through 51 Processing helix chain 'x' and resid 13 through 46 Processing helix chain 'y' and resid 14 through 38 Processing helix chain 'y' and resid 42 through 51 Processing helix chain 'z' and resid 14 through 46 Processing helix chain '5' and resid 14 through 38 Processing helix chain '5' and resid 42 through 51 Processing helix chain '4' and resid 14 through 46 Processing helix chain '6' and resid 1 through 10 removed outlier: 3.631A pdb=" N PHE 6 4 " --> pdb=" O MET 6 1 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR 6 5 " --> pdb=" O SER 6 2 " (cutoff:3.500A) Processing helix chain '6' and resid 12 through 38 removed outlier: 3.573A pdb=" N THR 6 38 " --> pdb=" O ILE 6 34 " (cutoff:3.500A) Processing helix chain 'aa' and resid 13 through 46 Processing helix chain 'Q' and resid 1 through 10 removed outlier: 3.630A pdb=" N PHE Q 4 " --> pdb=" O MET Q 1 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR Q 5 " --> pdb=" O SER Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 38 removed outlier: 3.574A 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 'ab' and resid 13 through 46 Processing helix chain 'c' and resid 9 through 13 removed outlier: 3.551A pdb=" N ASN c 12 " --> pdb=" O ASP c 9 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR c 13 " --> pdb=" O HIS c 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 9 through 13' Processing helix chain 'c' and resid 14 through 55 removed outlier: 4.396A pdb=" N ALA c 24 " --> pdb=" O ARG c 20 " (cutoff:3.500A) 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 11 through 13 removed outlier: 6.493A pdb=" N GLN M 11 " --> pdb=" O SER H 143 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS H 141 " --> pdb=" O ARG M 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 62 through 66 removed outlier: 4.475A 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: 5.619A pdb=" N VAL H 164 " --> pdb=" O GLU H 182 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU H 182 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP H 166 " --> pdb=" O GLU H 180 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASP H 170 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA H 176 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.730A 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 11 through 13 removed outlier: 6.589A 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: 4.475A 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: 5.618A pdb=" N VAL h 164 " --> pdb=" O GLU h 182 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU h 182 " --> pdb=" O VAL h 164 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP h 166 " --> pdb=" O GLU h 180 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASP h 170 " --> pdb=" O ALA h 176 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ALA h 176 " --> pdb=" O ASP h 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 131 through 133 removed outlier: 3.730A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 2122 hydrogen bonds defined for protein. 5994 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.88 Time building geometry restraints manager: 4.84 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: 9639 1.34 - 1.55: 27383 1.55 - 1.75: 385 1.75 - 1.96: 277 1.96 - 2.17: 204 Bond restraints: 37888 Sorted by residual: bond pdb=" C37 SPO t 102 " pdb=" C38 SPO t 102 " 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 p 102 " pdb=" C38 SPO p 102 " ideal model delta sigma weight residual 1.336 1.541 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C37 SPO b 101 " pdb=" C38 SPO b 101 " ideal model delta sigma weight residual 1.336 1.540 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C37 SPO 9 101 " pdb=" C38 SPO 9 101 " ideal model delta sigma weight residual 1.336 1.539 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C37 SPO D 102 " pdb=" C38 SPO D 102 " ideal model delta sigma weight residual 1.336 1.538 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 37883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.68: 51220 8.68 - 17.36: 830 17.36 - 26.05: 24 26.05 - 34.73: 0 34.73 - 43.41: 1 Bond angle restraints: 52075 Sorted by residual: angle pdb=" C16 BCL Q 602 " pdb=" C17 BCL Q 602 " pdb=" C18 BCL Q 602 " ideal model delta sigma weight residual 113.16 156.57 -43.41 5.53e+00 3.27e-02 6.17e+01 angle pdb=" C12 SPOab 102 " pdb=" C14 SPOab 102 " pdb=" C15 SPOab 102 " ideal model delta sigma weight residual 127.13 106.40 20.73 3.00e+00 1.11e-01 4.77e+01 angle pdb=" C10 SPO G 102 " pdb=" C9 SPO G 102 " pdb=" C7 SPO G 102 " ideal model delta sigma weight residual 127.14 106.85 20.29 3.00e+00 1.11e-01 4.58e+01 angle pdb=" C11 CDL m 406 " pdb=" CA5 CDL m 406 " pdb=" OA6 CDL m 406 " ideal model delta sigma weight residual 111.33 120.26 -8.93 1.32e+00 5.72e-01 4.57e+01 angle pdb=" C17 SPO 0 101 " pdb=" C19 SPO 0 101 " pdb=" C20 SPO 0 101 " ideal model delta sigma weight residual 127.83 107.74 20.09 3.00e+00 1.11e-01 4.48e+01 ... (remaining 52070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 19469 35.71 - 71.42: 823 71.42 - 107.13: 78 107.13 - 142.83: 6 142.83 - 178.54: 2 Dihedral angle restraints: 20378 sinusoidal: 9386 harmonic: 10992 Sorted by residual: dihedral pdb=" C31 U10 l 303 " pdb=" C32 U10 l 303 " pdb=" C33 U10 l 303 " pdb=" C34 U10 l 303 " ideal model delta sinusoidal sigma weight residual -97.88 80.66 -178.54 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C37 U10 l 303 " pdb=" C38 U10 l 303 " pdb=" C39 U10 l 303 " pdb=" C41 U10 l 303 " ideal model delta sinusoidal sigma weight residual -5.63 -154.19 148.56 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C11 U10 l 303 " pdb=" C8 U10 l 303 " pdb=" C9 U10 l 303 " pdb=" C7 U10 l 303 " ideal model delta sinusoidal sigma weight residual -179.95 -52.13 -127.82 1 2.00e+01 2.50e-03 3.87e+01 ... (remaining 20375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4430 0.061 - 0.122: 649 0.122 - 0.183: 42 0.183 - 0.244: 7 0.244 - 0.304: 3 Chirality restraints: 5131 Sorted by residual: chirality pdb=" CG LEU c 19 " pdb=" CB LEU c 19 " pdb=" CD1 LEU c 19 " pdb=" CD2 LEU c 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CG LEU L 21 " pdb=" CB LEU L 21 " pdb=" CD1 LEU L 21 " pdb=" CD2 LEU L 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2C BPH l 302 " pdb=" C1C BPH l 302 " pdb=" C3C BPH l 302 " pdb=" CMC BPH l 302 " both_signs ideal model delta sigma weight residual False -2.81 -2.53 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 5128 not shown) Planarity restraints: 6387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 SPO w 102 " 0.310 2.00e-02 2.50e+03 3.20e-01 1.28e+03 pdb=" C22 SPO w 102 " -0.275 2.00e-02 2.50e+03 pdb=" C23 SPO w 102 " -0.442 2.00e-02 2.50e+03 pdb=" C24 SPO w 102 " 0.026 2.00e-02 2.50e+03 pdb=" C25 SPO w 102 " 0.381 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C21 SPO 0 101 " 0.241 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C22 SPO 0 101 " -0.522 2.00e-02 2.50e+03 pdb=" C23 SPO 0 101 " 0.330 2.00e-02 2.50e+03 pdb=" C24 SPO 0 101 " -0.058 2.00e-02 2.50e+03 pdb=" C25 SPO 0 101 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 SPO 9 101 " 0.018 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C12 SPO 9 101 " 0.332 2.00e-02 2.50e+03 pdb=" C13 SPO 9 101 " -0.077 2.00e-02 2.50e+03 pdb=" C14 SPO 9 101 " -0.506 2.00e-02 2.50e+03 pdb=" C15 SPO 9 101 " 0.234 2.00e-02 2.50e+03 ... (remaining 6384 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 499 2.64 - 3.21: 31796 3.21 - 3.77: 57713 3.77 - 4.34: 82215 4.34 - 4.90: 134918 Nonbonded interactions: 307141 Sorted by model distance: nonbonded pdb=" C ILE 7 46 " pdb=" O LEU 6 44 " model vdw 2.077 3.270 nonbonded pdb=" OH TYR H 18 " pdb=" O14 PC1 H 602 " model vdw 2.118 3.040 nonbonded pdb=" O LEU 7 44 " pdb=" O TRP 6 43 " model vdw 2.141 3.040 nonbonded pdb=" O TRP 7 43 " pdb=" O LEU 6 44 " model vdw 2.155 3.040 nonbonded pdb=" OG1 THR a 38 " pdb=" O SER a 40 " model vdw 2.155 3.040 ... (remaining 307136 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 '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) selection = (chain 'n' and resid 12 through 49) selection = (chain 'p' and resid 12 through 49) selection = (chain 'r' and resid 12 through 49) selection = (chain 't' and resid 12 through 49) selection = (chain 'x' and resid 12 through 49) } ncs_group { reference = (chain '4' and resid 13 through 48) selection = (chain 'v' and resid 13 through 48) selection = (chain 'z' and resid 13 through 48) } ncs_group { reference = chain '5' selection = (chain 'K' and (resid 13 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 'O' and resid 13 through 101) selection = (chain 'w' and (resid 13 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 'y' } ncs_group { reference = chain '6' selection = chain '7' } ncs_group { reference = (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 'Q' 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 'u' and resid 1 through 54) } ncs_group { reference = (chain 'C' and (resid 6 through 69 or (resid 1201 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or name \ C2F or name C2G or name C2H or name C2I or name C3 or name C31 or name C32 or na \ me C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 o \ r name C3A or name C3B or name C3C or name O11 or name O12 or name O13 or name O \ 14 or name O21 or name O22 or name O31 or name O32 or name P )) or resid 1202)) selection = (chain 'c' and resid 6 through 1202) } ncs_group { reference = (chain 'H' and resid 1 through 601) selection = (chain 'h' and (resid 1 through 260 or (resid 301 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or na \ me C3C or name C3D or name C3E or name C3F or name C3G or name C3H or name O11 o \ r name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O \ 32 or name P )))) } ncs_group { reference = (chain 'L' and (resid 1 through 268 or resid 302 through 306)) selection = (chain 'l' and (resid 1 through 268 or (resid 301 and (name NB or name ND or nam \ e C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name C1A or name C1B or name C1C or name C1D or name C2 or name C2A \ or name C2B or name C2C or name C2D or name C3 or name C3A or name C3B or name C \ 3C or name C3D or name C4 or name C4A or name C4B or name C4C or name C4D or nam \ e C5 or name C6 or name C7 or name C8 or name C9 or name CAA or name CAB or name \ CAC or name CAD or name 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 CMC or name CMD or name NA or name NC or name O1A or name O \ 1D or name O2A or name O2D or name OBB or name OBD or name MG )) or resid 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 C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C \ 31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3M or na \ me 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 )) or (resid 304 and (name NB or name ND or \ name C1 or name C1A or name C1B or name C1C or name C1D or name C2 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 C4B or name C4C or name C4D or name CAA or name CAB or n \ ame CAC or name CAD or name 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 CMC or name CMD or name NA or name NC or name O1A or nam \ e O1D or name O2A or name O2D or name OBB or name OBD or name MG )) or resid 305 \ )) } ncs_group { reference = (chain 'M' and resid 2 through 306) selection = (chain 'm' and resid 2 through 306) } 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.730 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.090 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.023 0.570 37911 Z= 1.572 Angle : 1.972 43.412 52075 Z= 0.692 Chirality : 0.043 0.304 5131 Planarity : 0.046 0.320 6387 Dihedral : 17.305 178.542 13314 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.01 % Allowed : 5.35 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.13), residues: 3704 helix: 2.55 (0.10), residues: 2342 sheet: 0.65 (0.82), residues: 44 loop : -0.31 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG s 15 TYR 0.013 0.001 TYR l 164 PHE 0.025 0.002 PHE c 7 TRP 0.020 0.002 TRP l 263 HIS 0.007 0.001 HIS l 153 Details of bonding type rmsd covalent geometry : bond 0.01918 (37888) covalent geometry : angle 1.97160 (52075) hydrogen bonds : bond 0.11234 ( 2118) hydrogen bonds : angle 4.58165 ( 5994) Misc. bond : bond 0.51147 ( 23) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 756 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 73 TYR cc_start: 0.8025 (m-80) cc_final: 0.7768 (m-80) REVERT: L 193 LEU cc_start: 0.8535 (tp) cc_final: 0.8218 (tt) REVERT: L 248 MET cc_start: 0.8446 (mmm) cc_final: 0.8237 (mmp) REVERT: M 167 LEU cc_start: 0.8370 (mt) cc_final: 0.8074 (mt) REVERT: M 216 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8120 (t80) REVERT: H 46 ASP cc_start: 0.5723 (p0) cc_final: 0.5419 (p0) REVERT: H 62 LYS cc_start: 0.7579 (ptmt) cc_final: 0.7300 (mtpt) REVERT: H 124 ASP cc_start: 0.4950 (p0) cc_final: 0.4701 (p0) REVERT: H 255 MET cc_start: 0.5173 (mmt) cc_final: 0.4754 (ttm) REVERT: A 50 LYS cc_start: 0.6662 (tttt) cc_final: 0.6294 (ttmm) REVERT: A 52 ASN cc_start: 0.5732 (t0) cc_final: 0.5453 (t0) REVERT: D 33 LEU cc_start: 0.8369 (mt) cc_final: 0.8054 (mp) REVERT: F 8 TRP cc_start: 0.6489 (m100) cc_final: 0.5595 (m100) REVERT: G 25 MET cc_start: 0.6478 (mmm) cc_final: 0.5959 (mmm) REVERT: 9 10 ILE cc_start: 0.7845 (mm) cc_final: 0.7504 (mt) REVERT: 0 25 MET cc_start: 0.7164 (mmm) cc_final: 0.6913 (mmp) REVERT: l 213 ASP cc_start: 0.8608 (m-30) cc_final: 0.8281 (m-30) REVERT: m 15 PRO cc_start: 0.8185 (Cg_exo) cc_final: 0.7911 (Cg_endo) REVERT: m 214 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8643 (tp) REVERT: h 12 LEU cc_start: 0.8893 (tp) cc_final: 0.8650 (tp) REVERT: h 103 ASP cc_start: 0.8395 (t0) cc_final: 0.8110 (t0) REVERT: h 185 ASP cc_start: 0.7021 (m-30) cc_final: 0.6539 (t0) REVERT: h 195 MET cc_start: 0.7934 (mmm) cc_final: 0.7657 (mmt) REVERT: h 255 MET cc_start: 0.3095 (mmt) cc_final: 0.2560 (ttp) REVERT: e 9 TYR cc_start: 0.7398 (m-10) cc_final: 0.7049 (m-80) REVERT: k 1 MET cc_start: 0.0757 (mpp) cc_final: 0.0492 (ppp) REVERT: n 24 TYR cc_start: 0.6960 (t80) cc_final: 0.6725 (t80) REVERT: o 20 GLN cc_start: 0.7235 (tt0) cc_final: 0.6937 (tt0) REVERT: p 44 ILE cc_start: 0.8366 (mm) cc_final: 0.8085 (mt) REVERT: r 43 TYR cc_start: 0.8237 (t80) cc_final: 0.7776 (t80) REVERT: t 14 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.5785 (t0) REVERT: u 42 ASN cc_start: 0.7844 (t0) cc_final: 0.7418 (t0) REVERT: y 23 PHE cc_start: 0.3367 (OUTLIER) cc_final: 0.2937 (t80) REVERT: y 43 TRP cc_start: 0.5805 (p90) cc_final: 0.5566 (p90) REVERT: 5 23 PHE cc_start: 0.2987 (OUTLIER) cc_final: 0.1896 (t80) outliers start: 95 outliers final: 19 residues processed: 822 average time/residue: 0.2283 time to fit residues: 310.2500 Evaluate side-chains 575 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 551 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 214 LEU Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain t residue 14 ASP Chi-restraints excluded: chain u residue 16 VAL Chi-restraints excluded: chain w residue 44 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain c residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 168 HIS M 237 GLN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN E 21 HIS I 20 GLN N 21 HIS ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 18 GLN l 20 ASN l 199 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 HIS h 201 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN i 42 ASN j 21 HIS o 20 GLN y 20 GLN z 21 HIS Q 20 GLN c 8 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.182023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.153312 restraints weight = 46249.152| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.07 r_work: 0.3316 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37911 Z= 0.137 Angle : 0.711 13.525 52075 Z= 0.286 Chirality : 0.038 0.194 5131 Planarity : 0.004 0.038 6387 Dihedral : 16.853 175.372 6664 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.34 % Allowed : 10.16 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.14), residues: 3704 helix: 2.59 (0.10), residues: 2450 sheet: 1.08 (0.74), residues: 64 loop : -0.36 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG v 46 TYR 0.019 0.001 TYR o 41 PHE 0.025 0.001 PHE M 123 TRP 0.020 0.001 TRP z 48 HIS 0.015 0.002 HIS N 21 Details of bonding type rmsd covalent geometry : bond 0.00306 (37888) covalent geometry : angle 0.71084 (52075) hydrogen bonds : bond 0.05358 ( 2118) hydrogen bonds : angle 3.80338 ( 5994) Misc. bond : bond 0.00207 ( 23) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 598 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 193 LEU cc_start: 0.8452 (tp) cc_final: 0.8143 (tt) REVERT: M 165 PRO cc_start: 0.7820 (Cg_exo) cc_final: 0.7545 (Cg_endo) REVERT: H 255 MET cc_start: 0.5125 (mmt) cc_final: 0.4648 (ttm) REVERT: A 50 LYS cc_start: 0.7088 (tttt) cc_final: 0.6650 (ttmm) REVERT: A 52 ASN cc_start: 0.6350 (t0) cc_final: 0.6026 (t0) REVERT: D 8 TRP cc_start: 0.7699 (m100) cc_final: 0.7384 (m100) REVERT: D 33 LEU cc_start: 0.8360 (mt) cc_final: 0.8075 (mp) REVERT: F 8 TRP cc_start: 0.6583 (m100) cc_final: 0.5666 (m100) REVERT: F 9 MET cc_start: 0.5618 (mpp) cc_final: 0.4410 (mpp) REVERT: G 18 GLN cc_start: 0.6668 (pt0) cc_final: 0.6293 (pt0) REVERT: G 43 TYR cc_start: 0.6521 (t80) cc_final: 0.6220 (t80) REVERT: 7 9 MET cc_start: 0.7651 (mtm) cc_final: 0.7215 (mtt) REVERT: 0 25 MET cc_start: 0.7763 (mmm) cc_final: 0.7384 (mmp) REVERT: C 20 ARG cc_start: 0.7394 (ttm170) cc_final: 0.5986 (tmt170) REVERT: l 202 LYS cc_start: 0.8238 (tttt) cc_final: 0.7839 (mtpt) REVERT: l 213 ASP cc_start: 0.8856 (m-30) cc_final: 0.8551 (m-30) REVERT: m 15 PRO cc_start: 0.8357 (Cg_exo) cc_final: 0.8129 (Cg_endo) REVERT: h 255 MET cc_start: 0.3348 (mmt) cc_final: 0.2601 (ttp) REVERT: e 9 TYR cc_start: 0.7450 (m-10) cc_final: 0.7137 (m-80) REVERT: j 25 MET cc_start: 0.8113 (mmt) cc_final: 0.7810 (mmt) REVERT: k 1 MET cc_start: 0.0662 (mpp) cc_final: -0.0759 (ttt) REVERT: p 44 ILE cc_start: 0.8477 (mm) cc_final: 0.8174 (mt) REVERT: q 24 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7844 (mm) REVERT: u 1 MET cc_start: 0.3772 (tpp) cc_final: 0.1505 (tmm) REVERT: u 9 MET cc_start: 0.6100 (mpp) cc_final: 0.5710 (mmm) REVERT: x 44 ILE cc_start: 0.5824 (mm) cc_final: 0.5580 (mm) REVERT: y 23 PHE cc_start: 0.3552 (OUTLIER) cc_final: 0.3267 (t80) REVERT: y 43 TRP cc_start: 0.6293 (p90) cc_final: 0.5915 (p90) REVERT: 5 23 PHE cc_start: 0.2874 (OUTLIER) cc_final: 0.1891 (t80) outliers start: 74 outliers final: 39 residues processed: 637 average time/residue: 0.2246 time to fit residues: 239.0523 Evaluate side-chains 569 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 527 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain 8 residue 14 ASP Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 12 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain u residue 16 VAL Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 27 MET Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 347 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 266 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 331 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 18 GLN l 199 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 199 GLN h 201 ASN d 20 GLN f 20 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 16 GLN k 20 GLN u 20 GLN x 21 HIS ** x 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.169498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.137679 restraints weight = 46661.358| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.22 r_work: 0.3129 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 37911 Z= 0.311 Angle : 0.932 15.871 52075 Z= 0.380 Chirality : 0.046 0.328 5131 Planarity : 0.005 0.069 6387 Dihedral : 17.330 169.627 6649 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.99 % Allowed : 12.15 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.13), residues: 3704 helix: 1.80 (0.10), residues: 2456 sheet: -0.70 (0.65), residues: 68 loop : -0.64 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 15 TYR 0.020 0.002 TYR N 43 PHE 0.048 0.003 PHE L 216 TRP 0.031 0.002 TRP 7 43 HIS 0.014 0.002 HIS N 39 Details of bonding type rmsd covalent geometry : bond 0.00758 (37888) covalent geometry : angle 0.93216 (52075) hydrogen bonds : bond 0.06935 ( 2118) hydrogen bonds : angle 4.16524 ( 5994) Misc. bond : bond 0.00399 ( 23) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 573 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 254 ILE cc_start: 0.6038 (OUTLIER) cc_final: 0.5567 (pt) REVERT: M 25 ASN cc_start: 0.5404 (t0) cc_final: 0.4786 (m-40) REVERT: M 129 TRP cc_start: 0.7296 (t-100) cc_final: 0.7025 (t-100) REVERT: M 165 PRO cc_start: 0.7818 (Cg_exo) cc_final: 0.7442 (Cg_endo) REVERT: M 216 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8375 (t80) REVERT: M 228 ARG cc_start: 0.7805 (ptp-170) cc_final: 0.7533 (ptp-170) REVERT: H 70 ARG cc_start: 0.6222 (mmt90) cc_final: 0.5605 (mmm160) REVERT: H 118 ARG cc_start: 0.5756 (mtt180) cc_final: 0.4307 (mmm160) REVERT: H 255 MET cc_start: 0.5419 (mmt) cc_final: 0.4740 (ttm) REVERT: A 50 LYS cc_start: 0.7733 (tttt) cc_final: 0.6891 (ttmm) REVERT: A 52 ASN cc_start: 0.7234 (t0) cc_final: 0.6811 (t0) REVERT: B 16 GLN cc_start: 0.6720 (mt0) cc_final: 0.6501 (mt0) REVERT: D 33 LEU cc_start: 0.8579 (mt) cc_final: 0.8254 (mp) REVERT: F 8 TRP cc_start: 0.6591 (m100) cc_final: 0.6130 (m100) REVERT: F 9 MET cc_start: 0.5729 (mpp) cc_final: 0.5447 (mmt) REVERT: J 15 GLU cc_start: 0.4175 (OUTLIER) cc_final: 0.3715 (mm-30) REVERT: C 20 ARG cc_start: 0.8007 (ttm170) cc_final: 0.6597 (tmt170) REVERT: C 43 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7959 (mp) REVERT: l 82 LYS cc_start: 0.8886 (mttp) cc_final: 0.8572 (mtmt) REVERT: l 199 ASN cc_start: 0.8813 (m-40) cc_final: 0.8576 (m110) REVERT: l 202 LYS cc_start: 0.8240 (tttt) cc_final: 0.7968 (ptmt) REVERT: l 213 ASP cc_start: 0.8900 (m-30) cc_final: 0.8579 (m-30) REVERT: m 15 PRO cc_start: 0.8389 (Cg_exo) cc_final: 0.8101 (Cg_endo) REVERT: h 166 ASP cc_start: 0.7510 (t0) cc_final: 0.7204 (t0) REVERT: h 255 MET cc_start: 0.3857 (mmt) cc_final: 0.2809 (ttp) REVERT: e 9 TYR cc_start: 0.7751 (m-80) cc_final: 0.7485 (m-80) REVERT: f 27 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8919 (tp) REVERT: g 18 GLN cc_start: 0.8232 (mp10) cc_final: 0.7390 (mp10) REVERT: j 15 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5565 (tt0) REVERT: k 47 SER cc_start: 0.8543 (t) cc_final: 0.8293 (p) REVERT: o 15 ARG cc_start: 0.5739 (mtp180) cc_final: 0.5218 (mtp85) REVERT: p 44 ILE cc_start: 0.8683 (mm) cc_final: 0.8376 (mt) REVERT: q 24 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8064 (mm) REVERT: u 1 MET cc_start: 0.4491 (tpp) cc_final: 0.1487 (tmm) REVERT: v 20 LEU cc_start: 0.7266 (tp) cc_final: 0.7019 (tp) REVERT: y 23 PHE cc_start: 0.3850 (OUTLIER) cc_final: 0.3483 (t80) REVERT: 5 23 PHE cc_start: 0.2908 (OUTLIER) cc_final: 0.2045 (t80) outliers start: 126 outliers final: 66 residues processed: 651 average time/residue: 0.2223 time to fit residues: 240.7263 Evaluate side-chains 613 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 538 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 ILE Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 TRP Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 220 VAL Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 12 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 80 SER Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain b residue 37 VAL Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 42 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain j residue 15 GLU Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain 5 residue 27 LEU Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 150 optimal weight: 0.9990 chunk 300 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 152 optimal weight: 30.0000 chunk 303 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 265 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 173 HIS ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 18 GLN l 20 ASN m 77 GLN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN Q 20 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.175147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.143984 restraints weight = 45862.430| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.11 r_work: 0.3226 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.266 37911 Z= 0.188 Angle : 0.680 13.084 52075 Z= 0.275 Chirality : 0.037 0.178 5131 Planarity : 0.004 0.057 6387 Dihedral : 16.019 151.129 6645 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.40 % Allowed : 14.17 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.14), residues: 3704 helix: 2.42 (0.10), residues: 2449 sheet: -0.06 (0.62), residues: 88 loop : -0.49 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG l 109 TYR 0.017 0.001 TYR d 5 PHE 0.024 0.001 PHE L 216 TRP 0.022 0.001 TRP l 271 HIS 0.008 0.001 HIS m 266 Details of bonding type rmsd covalent geometry : bond 0.00285 (37888) covalent geometry : angle 0.68000 (52075) hydrogen bonds : bond 0.05073 ( 2118) hydrogen bonds : angle 3.79199 ( 5994) Misc. bond : bond 0.05541 ( 23) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 583 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: L 212 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6917 (mm-30) REVERT: M 25 ASN cc_start: 0.5322 (t0) cc_final: 0.4747 (m-40) REVERT: M 111 GLU cc_start: 0.5426 (mm-30) cc_final: 0.5144 (mm-30) REVERT: M 165 PRO cc_start: 0.7818 (Cg_exo) cc_final: 0.7519 (Cg_endo) REVERT: M 216 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8006 (t80) REVERT: H 46 ASP cc_start: 0.6009 (p0) cc_final: 0.5259 (p0) REVERT: H 62 LYS cc_start: 0.7488 (mtpt) cc_final: 0.7277 (mtpt) REVERT: H 70 ARG cc_start: 0.6190 (mmt90) cc_final: 0.5577 (mmm160) REVERT: H 118 ARG cc_start: 0.5470 (mtt180) cc_final: 0.4200 (mmm160) REVERT: H 255 MET cc_start: 0.5264 (mmt) cc_final: 0.4642 (ttm) REVERT: A 50 LYS cc_start: 0.7576 (tttt) cc_final: 0.7046 (ttmm) REVERT: A 52 ASN cc_start: 0.7014 (t0) cc_final: 0.6641 (t0) REVERT: D 33 LEU cc_start: 0.8474 (mt) cc_final: 0.8029 (mp) REVERT: F 8 TRP cc_start: 0.6578 (m100) cc_final: 0.6085 (m100) REVERT: F 9 MET cc_start: 0.5612 (mpp) cc_final: 0.5385 (mmt) REVERT: C 20 ARG cc_start: 0.7626 (ttm170) cc_final: 0.6323 (tmt170) REVERT: l 82 LYS cc_start: 0.8738 (mttp) cc_final: 0.8452 (mtmt) REVERT: l 202 LYS cc_start: 0.8228 (tttt) cc_final: 0.7967 (ptmt) REVERT: l 213 ASP cc_start: 0.8854 (m-30) cc_final: 0.8607 (m-30) REVERT: h 200 SER cc_start: 0.7453 (p) cc_final: 0.7130 (m) REVERT: h 255 MET cc_start: 0.3693 (mmt) cc_final: 0.2819 (ttp) REVERT: e 9 TYR cc_start: 0.7546 (m-80) cc_final: 0.7253 (m-80) REVERT: g 18 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7860 (mm-40) REVERT: j 25 MET cc_start: 0.8026 (mmt) cc_final: 0.7758 (mmt) REVERT: p 44 ILE cc_start: 0.8552 (mm) cc_final: 0.8221 (mt) REVERT: q 24 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8017 (mm) REVERT: u 1 MET cc_start: 0.4413 (tpp) cc_final: 0.1674 (tmm) REVERT: u 26 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8086 (tt) REVERT: w 41 TYR cc_start: 0.7991 (m-80) cc_final: 0.7398 (m-80) REVERT: y 23 PHE cc_start: 0.3978 (OUTLIER) cc_final: 0.3670 (t80) REVERT: 5 23 PHE cc_start: 0.3016 (OUTLIER) cc_final: 0.2032 (t80) REVERT: 6 45 GLU cc_start: 0.5620 (mm-30) cc_final: 0.5185 (mp0) outliers start: 76 outliers final: 42 residues processed: 629 average time/residue: 0.2235 time to fit residues: 234.6582 Evaluate side-chains 575 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 526 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain e residue 26 SER Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain 6 residue 26 LEU Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 6 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 327 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 chunk 296 optimal weight: 8.9990 chunk 1 optimal weight: 0.0000 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN K 20 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 18 GLN l 199 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN c 66 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.172663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.140609 restraints weight = 46045.025| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.16 r_work: 0.3180 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37911 Z= 0.166 Angle : 0.727 13.928 52075 Z= 0.294 Chirality : 0.039 0.231 5131 Planarity : 0.004 0.042 6387 Dihedral : 15.822 143.198 6639 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.01 % Allowed : 14.90 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.14), residues: 3704 helix: 2.35 (0.10), residues: 2455 sheet: -0.19 (0.62), residues: 88 loop : -0.51 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 6 15 TYR 0.023 0.001 TYR L 169 PHE 0.030 0.002 PHE L 216 TRP 0.022 0.001 TRP x 48 HIS 0.009 0.001 HIS m 182 Details of bonding type rmsd covalent geometry : bond 0.00392 (37888) covalent geometry : angle 0.72669 (52075) hydrogen bonds : bond 0.05452 ( 2118) hydrogen bonds : angle 3.82205 ( 5994) Misc. bond : bond 0.00229 ( 23) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 553 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: L 193 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7542 (tt) REVERT: L 212 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6570 (mm-30) REVERT: L 216 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5848 (t80) REVERT: L 248 MET cc_start: 0.8634 (tpp) cc_final: 0.8254 (tpt) REVERT: L 254 ILE cc_start: 0.5861 (OUTLIER) cc_final: 0.5416 (pt) REVERT: M 25 ASN cc_start: 0.5250 (t0) cc_final: 0.4753 (m-40) REVERT: M 111 GLU cc_start: 0.5820 (mm-30) cc_final: 0.5456 (mm-30) REVERT: M 129 TRP cc_start: 0.7208 (t-100) cc_final: 0.6967 (t-100) REVERT: M 165 PRO cc_start: 0.7825 (Cg_exo) cc_final: 0.7511 (Cg_endo) REVERT: M 216 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8081 (t80) REVERT: H 70 ARG cc_start: 0.6086 (mmt90) cc_final: 0.5429 (mmm160) REVERT: H 117 ARG cc_start: 0.6810 (mmm-85) cc_final: 0.6495 (mmm160) REVERT: H 118 ARG cc_start: 0.5467 (mtt180) cc_final: 0.4469 (mmt180) REVERT: H 175 MET cc_start: 0.6986 (ptt) cc_final: 0.6609 (mmt) REVERT: H 255 MET cc_start: 0.5275 (mmt) cc_final: 0.4716 (ttm) REVERT: A 5 TYR cc_start: 0.7527 (p90) cc_final: 0.7310 (p90) REVERT: A 50 LYS cc_start: 0.7701 (tttt) cc_final: 0.7046 (ttmm) REVERT: A 52 ASN cc_start: 0.7127 (t0) cc_final: 0.6819 (t0) REVERT: D 33 LEU cc_start: 0.8476 (mt) cc_final: 0.8052 (mp) REVERT: F 8 TRP cc_start: 0.6568 (m100) cc_final: 0.6094 (m100) REVERT: G 44 ILE cc_start: 0.7342 (mm) cc_final: 0.7103 (mm) REVERT: 0 14 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7313 (t0) REVERT: C 20 ARG cc_start: 0.7696 (ttm170) cc_final: 0.6379 (tmt170) REVERT: l 82 LYS cc_start: 0.8851 (mttp) cc_final: 0.8533 (mtmt) REVERT: l 202 LYS cc_start: 0.8213 (tttt) cc_final: 0.7960 (ptmt) REVERT: l 213 ASP cc_start: 0.8869 (m-30) cc_final: 0.8620 (m-30) REVERT: h 12 LEU cc_start: 0.8974 (tp) cc_final: 0.8725 (tp) REVERT: h 80 SER cc_start: 0.5919 (OUTLIER) cc_final: 0.5511 (m) REVERT: h 218 THR cc_start: 0.8136 (p) cc_final: 0.7764 (t) REVERT: h 255 MET cc_start: 0.3758 (mmt) cc_final: 0.2879 (ttp) REVERT: e 9 TYR cc_start: 0.7605 (m-80) cc_final: 0.7342 (m-80) REVERT: g 18 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: p 44 ILE cc_start: 0.8594 (mm) cc_final: 0.8271 (mt) REVERT: q 24 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7962 (mm) REVERT: u 1 MET cc_start: 0.4600 (tpp) cc_final: 0.1802 (tmm) REVERT: u 26 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8132 (tp) REVERT: w 41 TYR cc_start: 0.8138 (m-80) cc_final: 0.7516 (m-80) REVERT: y 23 PHE cc_start: 0.3930 (OUTLIER) cc_final: 0.3643 (t80) REVERT: 5 23 PHE cc_start: 0.2932 (OUTLIER) cc_final: 0.2039 (t80) outliers start: 95 outliers final: 56 residues processed: 614 average time/residue: 0.2214 time to fit residues: 227.0380 Evaluate side-chains 591 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 523 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 196 SER Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 7 residue 36 LEU Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 14 ASP Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 220 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 12 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 80 SER Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 34 ILE Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain 4 residue 29 TRP Chi-restraints excluded: chain 6 residue 26 LEU Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 67 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 chunk 287 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 338 optimal weight: 0.9990 chunk 319 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 18 GLN l 199 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 16 GLN ** x 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.182986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.152804 restraints weight = 45506.390| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.11 r_work: 0.3196 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37911 Z= 0.134 Angle : 0.670 12.838 52075 Z= 0.272 Chirality : 0.038 0.197 5131 Planarity : 0.003 0.039 6387 Dihedral : 15.465 142.642 6639 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.72 % Allowed : 15.47 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.14), residues: 3704 helix: 2.50 (0.10), residues: 2453 sheet: -0.13 (0.61), residues: 88 loop : -0.43 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l 109 TYR 0.017 0.001 TYR 0 24 PHE 0.025 0.001 PHE L 216 TRP 0.028 0.001 TRP x 48 HIS 0.013 0.001 HIS N 39 Details of bonding type rmsd covalent geometry : bond 0.00305 (37888) covalent geometry : angle 0.67014 (52075) hydrogen bonds : bond 0.04999 ( 2118) hydrogen bonds : angle 3.76658 ( 5994) Misc. bond : bond 0.00185 ( 23) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 554 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: L 212 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6682 (mm-30) REVERT: L 216 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.5853 (t80) REVERT: L 248 MET cc_start: 0.8575 (tpp) cc_final: 0.8249 (tpt) REVERT: M 25 ASN cc_start: 0.5263 (t0) cc_final: 0.4630 (m-40) REVERT: M 111 GLU cc_start: 0.5715 (mm-30) cc_final: 0.5415 (mm-30) REVERT: M 129 TRP cc_start: 0.7249 (t-100) cc_final: 0.7029 (t-100) REVERT: M 165 PRO cc_start: 0.7693 (Cg_exo) cc_final: 0.7364 (Cg_endo) REVERT: M 216 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7981 (t80) REVERT: H 70 ARG cc_start: 0.6000 (mmt90) cc_final: 0.5250 (mmm160) REVERT: H 117 ARG cc_start: 0.6712 (mmm-85) cc_final: 0.6481 (mmm160) REVERT: H 118 ARG cc_start: 0.5323 (mtt180) cc_final: 0.4334 (mmt180) REVERT: H 175 MET cc_start: 0.6919 (ptt) cc_final: 0.6384 (mmt) REVERT: H 255 MET cc_start: 0.5221 (mmt) cc_final: 0.4682 (ttt) REVERT: A 50 LYS cc_start: 0.7691 (tttt) cc_final: 0.7082 (ttmm) REVERT: A 52 ASN cc_start: 0.6984 (t0) cc_final: 0.6672 (t0) REVERT: D 33 LEU cc_start: 0.8461 (mt) cc_final: 0.8027 (mp) REVERT: F 8 TRP cc_start: 0.6462 (m100) cc_final: 0.5937 (m100) REVERT: G 44 ILE cc_start: 0.7253 (mm) cc_final: 0.7030 (mm) REVERT: J 25 MET cc_start: 0.6762 (mmm) cc_final: 0.6547 (mmm) REVERT: 0 14 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7298 (t0) REVERT: C 20 ARG cc_start: 0.7615 (ttm170) cc_final: 0.6214 (tmt170) REVERT: l 82 LYS cc_start: 0.8733 (mttp) cc_final: 0.8440 (mtmt) REVERT: l 202 LYS cc_start: 0.8280 (tttt) cc_final: 0.8024 (ptmt) REVERT: l 213 ASP cc_start: 0.8770 (m-30) cc_final: 0.8545 (m-30) REVERT: l 216 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8150 (t80) REVERT: h 218 THR cc_start: 0.8133 (p) cc_final: 0.7766 (t) REVERT: h 255 MET cc_start: 0.3594 (mmt) cc_final: 0.2858 (ttp) REVERT: e 9 TYR cc_start: 0.7566 (m-80) cc_final: 0.7311 (m-80) REVERT: p 44 ILE cc_start: 0.8498 (mm) cc_final: 0.8181 (mt) REVERT: q 24 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7898 (mm) REVERT: u 1 MET cc_start: 0.4680 (tpp) cc_final: 0.1900 (tmm) REVERT: u 26 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8027 (tp) REVERT: v 43 TYR cc_start: 0.7880 (t80) cc_final: 0.7510 (t80) REVERT: w 41 TYR cc_start: 0.7996 (m-80) cc_final: 0.7312 (m-80) REVERT: y 23 PHE cc_start: 0.3967 (OUTLIER) cc_final: 0.3720 (t80) REVERT: y 43 TRP cc_start: 0.6867 (p90) cc_final: 0.6494 (p90) REVERT: 5 23 PHE cc_start: 0.2908 (OUTLIER) cc_final: 0.2082 (t80) REVERT: c 57 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.7919 (mm) outliers start: 86 outliers final: 54 residues processed: 604 average time/residue: 0.2196 time to fit residues: 221.5998 Evaluate side-chains 589 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 525 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 196 SER Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 7 residue 36 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 14 ASP Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain l residue 220 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 305 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 283 optimal weight: 0.8980 chunk 69 optimal weight: 0.0270 chunk 174 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 GLN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 16 GLN 0 18 GLN l 199 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN c 66 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.180723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.147686 restraints weight = 46005.959| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.28 r_work: 0.3192 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37911 Z= 0.114 Angle : 0.631 12.568 52075 Z= 0.258 Chirality : 0.037 0.217 5131 Planarity : 0.003 0.039 6387 Dihedral : 15.045 137.764 6639 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.44 % Allowed : 15.60 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.14), residues: 3704 helix: 2.60 (0.10), residues: 2465 sheet: -0.04 (0.62), residues: 88 loop : -0.42 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l 109 TYR 0.018 0.001 TYR 0 24 PHE 0.028 0.001 PHE m 216 TRP 0.024 0.001 TRP x 48 HIS 0.010 0.001 HIS N 39 Details of bonding type rmsd covalent geometry : bond 0.00250 (37888) covalent geometry : angle 0.63130 (52075) hydrogen bonds : bond 0.04647 ( 2118) hydrogen bonds : angle 3.68469 ( 5994) Misc. bond : bond 0.00147 ( 23) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 550 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: L 212 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6746 (mm-30) REVERT: L 216 PHE cc_start: 0.6122 (OUTLIER) cc_final: 0.5900 (t80) REVERT: M 25 ASN cc_start: 0.5340 (t0) cc_final: 0.4698 (m-40) REVERT: M 165 PRO cc_start: 0.7684 (Cg_exo) cc_final: 0.7365 (Cg_endo) REVERT: M 216 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7852 (t80) REVERT: H 7 PHE cc_start: 0.8004 (p90) cc_final: 0.7442 (p90) REVERT: H 70 ARG cc_start: 0.5998 (mmt90) cc_final: 0.5341 (mmm160) REVERT: H 117 ARG cc_start: 0.6855 (mmm-85) cc_final: 0.6522 (mmm160) REVERT: H 118 ARG cc_start: 0.5198 (mtt180) cc_final: 0.4182 (mmt180) REVERT: H 175 MET cc_start: 0.6873 (ptt) cc_final: 0.6344 (mmt) REVERT: H 255 MET cc_start: 0.5247 (mmt) cc_final: 0.4746 (ttt) REVERT: A 50 LYS cc_start: 0.7583 (tttt) cc_final: 0.7052 (ttmm) REVERT: A 52 ASN cc_start: 0.7002 (t0) cc_final: 0.6684 (t0) REVERT: D 33 LEU cc_start: 0.8392 (mt) cc_final: 0.7900 (mp) REVERT: F 8 TRP cc_start: 0.6387 (m100) cc_final: 0.6107 (m100) REVERT: G 44 ILE cc_start: 0.7258 (mm) cc_final: 0.7038 (mm) REVERT: O 30 MET cc_start: 0.3306 (mmt) cc_final: 0.2930 (mmm) REVERT: 9 27 LEU cc_start: 0.8958 (tp) cc_final: 0.8681 (tp) REVERT: 0 14 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7187 (t0) REVERT: C 20 ARG cc_start: 0.7390 (ttm170) cc_final: 0.5940 (tmt170) REVERT: C 28 MET cc_start: 0.7795 (ttt) cc_final: 0.7587 (ttt) REVERT: l 59 TRP cc_start: 0.8472 (m100) cc_final: 0.8214 (m100) REVERT: l 82 LYS cc_start: 0.8768 (mttp) cc_final: 0.8471 (mtmt) REVERT: l 202 LYS cc_start: 0.8264 (tttt) cc_final: 0.7999 (ptmt) REVERT: l 213 ASP cc_start: 0.8845 (m-30) cc_final: 0.8572 (m-30) REVERT: l 216 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8141 (t80) REVERT: h 218 THR cc_start: 0.8142 (p) cc_final: 0.7794 (t) REVERT: h 255 MET cc_start: 0.3489 (mmt) cc_final: 0.2807 (ttp) REVERT: e 9 TYR cc_start: 0.7567 (m-80) cc_final: 0.7313 (m-80) REVERT: p 44 ILE cc_start: 0.8413 (mm) cc_final: 0.8132 (mt) REVERT: q 24 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7891 (mm) REVERT: u 1 MET cc_start: 0.4715 (tpp) cc_final: 0.1916 (tmm) REVERT: u 26 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7939 (tt) REVERT: v 32 SER cc_start: 0.8469 (t) cc_final: 0.8137 (m) REVERT: v 43 TYR cc_start: 0.7861 (t80) cc_final: 0.7516 (t80) REVERT: v 44 ILE cc_start: 0.7883 (mm) cc_final: 0.7539 (mt) REVERT: w 41 TYR cc_start: 0.7940 (m-80) cc_final: 0.7371 (m-80) REVERT: y 23 PHE cc_start: 0.4026 (OUTLIER) cc_final: 0.3718 (t80) REVERT: y 43 TRP cc_start: 0.6931 (p90) cc_final: 0.6547 (p90) REVERT: 5 23 PHE cc_start: 0.3271 (OUTLIER) cc_final: 0.2457 (t80) outliers start: 77 outliers final: 51 residues processed: 595 average time/residue: 0.2266 time to fit residues: 224.2997 Evaluate side-chains 587 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 527 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 14 ASP Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain v residue 37 VAL Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 206 optimal weight: 0.7980 chunk 265 optimal weight: 0.9990 chunk 352 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 52 ASN l 199 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN ** x 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.179839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.146398 restraints weight = 45763.761| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.33 r_work: 0.3177 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37911 Z= 0.123 Angle : 0.646 12.694 52075 Z= 0.266 Chirality : 0.037 0.184 5131 Planarity : 0.003 0.036 6387 Dihedral : 14.905 138.296 6639 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.31 % Allowed : 16.01 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.14), residues: 3704 helix: 2.58 (0.10), residues: 2489 sheet: -0.03 (0.62), residues: 88 loop : -0.30 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l 109 TYR 0.019 0.001 TYR 0 24 PHE 0.028 0.001 PHE m 216 TRP 0.029 0.001 TRP x 48 HIS 0.018 0.001 HIS n 21 Details of bonding type rmsd covalent geometry : bond 0.00276 (37888) covalent geometry : angle 0.64614 (52075) hydrogen bonds : bond 0.04758 ( 2118) hydrogen bonds : angle 3.70811 ( 5994) Misc. bond : bond 0.00158 ( 23) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 537 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: L 212 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6765 (mm-30) REVERT: L 216 PHE cc_start: 0.6146 (OUTLIER) cc_final: 0.5901 (t80) REVERT: M 25 ASN cc_start: 0.5257 (t0) cc_final: 0.4660 (m-40) REVERT: M 165 PRO cc_start: 0.7674 (Cg_exo) cc_final: 0.7352 (Cg_endo) REVERT: M 216 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7863 (t80) REVERT: H 7 PHE cc_start: 0.8038 (p90) cc_final: 0.7485 (p90) REVERT: H 46 ASP cc_start: 0.5915 (p0) cc_final: 0.5150 (p0) REVERT: H 70 ARG cc_start: 0.6018 (mmt90) cc_final: 0.5405 (mmm160) REVERT: H 117 ARG cc_start: 0.6821 (mmm-85) cc_final: 0.6538 (mmm160) REVERT: H 118 ARG cc_start: 0.5190 (mtt180) cc_final: 0.4136 (mmt180) REVERT: H 175 MET cc_start: 0.6845 (ptt) cc_final: 0.6325 (mmt) REVERT: H 255 MET cc_start: 0.5239 (mmt) cc_final: 0.4747 (ttt) REVERT: A 50 LYS cc_start: 0.7579 (tttt) cc_final: 0.7023 (ttmm) REVERT: A 52 ASN cc_start: 0.6975 (t0) cc_final: 0.6636 (t0) REVERT: D 33 LEU cc_start: 0.8376 (mt) cc_final: 0.7886 (mp) REVERT: F 8 TRP cc_start: 0.6240 (m100) cc_final: 0.5986 (m100) REVERT: G 18 GLN cc_start: 0.6333 (pt0) cc_final: 0.5944 (pt0) REVERT: G 44 ILE cc_start: 0.7229 (mm) cc_final: 0.7010 (mm) REVERT: N 25 MET cc_start: 0.5046 (mpp) cc_final: 0.4522 (mpp) REVERT: 9 27 LEU cc_start: 0.8820 (tp) cc_final: 0.8360 (mt) REVERT: 0 14 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7192 (t70) REVERT: C 20 ARG cc_start: 0.7537 (ttm170) cc_final: 0.6018 (tmt170) REVERT: C 28 MET cc_start: 0.7797 (ttt) cc_final: 0.7550 (ttt) REVERT: l 82 LYS cc_start: 0.8795 (mttp) cc_final: 0.8496 (mtmt) REVERT: l 202 LYS cc_start: 0.8268 (tttt) cc_final: 0.8014 (ptmt) REVERT: l 213 ASP cc_start: 0.8857 (m-30) cc_final: 0.8584 (m-30) REVERT: l 216 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7953 (t80) REVERT: h 218 THR cc_start: 0.8145 (p) cc_final: 0.7780 (t) REVERT: h 255 MET cc_start: 0.3496 (mmt) cc_final: 0.2808 (ttp) REVERT: e 9 TYR cc_start: 0.7551 (m-80) cc_final: 0.7310 (m-80) REVERT: p 44 ILE cc_start: 0.8367 (mm) cc_final: 0.8098 (mt) REVERT: q 24 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7894 (mm) REVERT: u 1 MET cc_start: 0.4745 (tpp) cc_final: 0.1896 (tmm) REVERT: u 26 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7964 (tt) REVERT: v 32 SER cc_start: 0.8478 (t) cc_final: 0.8152 (m) REVERT: v 43 TYR cc_start: 0.7838 (t80) cc_final: 0.7467 (t80) REVERT: v 44 ILE cc_start: 0.7928 (mm) cc_final: 0.7592 (mt) REVERT: w 41 TYR cc_start: 0.7917 (m-80) cc_final: 0.7268 (m-80) REVERT: y 23 PHE cc_start: 0.4090 (OUTLIER) cc_final: 0.3765 (t80) REVERT: y 43 TRP cc_start: 0.6996 (p90) cc_final: 0.6590 (p90) REVERT: z 46 ARG cc_start: 0.4781 (tmt170) cc_final: 0.3635 (mpt180) REVERT: 5 23 PHE cc_start: 0.3257 (OUTLIER) cc_final: 0.2457 (t80) REVERT: 6 45 GLU cc_start: 0.5724 (mp0) cc_final: 0.5421 (mp0) REVERT: c 57 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7894 (mm) outliers start: 73 outliers final: 51 residues processed: 581 average time/residue: 0.2253 time to fit residues: 218.2207 Evaluate side-chains 587 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 526 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 196 SER Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 14 ASP Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain l residue 220 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain ab residue 25 MET Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 57 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 293 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 279 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 188 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 52 ASN l 199 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN ** x 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN c 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.181175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.148935 restraints weight = 45852.571| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.26 r_work: 0.3205 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37911 Z= 0.112 Angle : 0.625 12.559 52075 Z= 0.259 Chirality : 0.037 0.192 5131 Planarity : 0.003 0.036 6387 Dihedral : 14.706 138.247 6639 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.34 % Allowed : 15.85 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.14), residues: 3704 helix: 2.64 (0.10), residues: 2493 sheet: 0.01 (0.62), residues: 88 loop : -0.24 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l 109 TYR 0.019 0.001 TYR 0 24 PHE 0.025 0.001 PHE m 216 TRP 0.026 0.001 TRP x 48 HIS 0.012 0.001 HIS n 21 Details of bonding type rmsd covalent geometry : bond 0.00245 (37888) covalent geometry : angle 0.62542 (52075) hydrogen bonds : bond 0.04577 ( 2118) hydrogen bonds : angle 3.67579 ( 5994) Misc. bond : bond 0.00140 ( 23) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 545 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: L 216 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5915 (t80) REVERT: M 25 ASN cc_start: 0.5077 (t0) cc_final: 0.4606 (m-40) REVERT: M 165 PRO cc_start: 0.7656 (Cg_exo) cc_final: 0.7330 (Cg_endo) REVERT: M 166 ILE cc_start: 0.8352 (mt) cc_final: 0.7996 (mt) REVERT: M 216 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7785 (t80) REVERT: H 7 PHE cc_start: 0.7990 (p90) cc_final: 0.7420 (p90) REVERT: H 46 ASP cc_start: 0.5878 (p0) cc_final: 0.5129 (p0) REVERT: H 117 ARG cc_start: 0.6860 (mmm-85) cc_final: 0.6654 (mmm160) REVERT: H 118 ARG cc_start: 0.5170 (mtt180) cc_final: 0.3731 (mmm160) REVERT: H 175 MET cc_start: 0.6685 (ptt) cc_final: 0.6250 (mmt) REVERT: H 255 MET cc_start: 0.5166 (mmt) cc_final: 0.4719 (ttt) REVERT: A 50 LYS cc_start: 0.7546 (tttt) cc_final: 0.6993 (ttmm) REVERT: A 52 ASN cc_start: 0.6916 (t0) cc_final: 0.6582 (t0) REVERT: D 33 LEU cc_start: 0.8368 (mt) cc_final: 0.7872 (mp) REVERT: F 8 TRP cc_start: 0.6081 (m100) cc_final: 0.5795 (m100) REVERT: G 18 GLN cc_start: 0.6313 (pt0) cc_final: 0.5874 (pt0) REVERT: G 43 TYR cc_start: 0.6591 (t80) cc_final: 0.6293 (t80) REVERT: G 44 ILE cc_start: 0.7200 (mm) cc_final: 0.6965 (mm) REVERT: N 25 MET cc_start: 0.5016 (mpp) cc_final: 0.3720 (mpp) REVERT: O 30 MET cc_start: 0.3361 (mmt) cc_final: 0.2938 (mmm) REVERT: 7 10 ILE cc_start: 0.7090 (mm) cc_final: 0.6874 (mt) REVERT: C 20 ARG cc_start: 0.7473 (ttm170) cc_final: 0.5995 (tmt170) REVERT: C 28 MET cc_start: 0.7786 (ttt) cc_final: 0.7524 (ttt) REVERT: l 82 LYS cc_start: 0.8733 (mttp) cc_final: 0.8448 (mtmt) REVERT: l 202 LYS cc_start: 0.8244 (tttt) cc_final: 0.8004 (ptmt) REVERT: l 213 ASP cc_start: 0.8836 (m-30) cc_final: 0.8559 (m-30) REVERT: l 216 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7846 (t80) REVERT: h 218 THR cc_start: 0.8126 (p) cc_final: 0.7788 (t) REVERT: h 255 MET cc_start: 0.3425 (mmt) cc_final: 0.2762 (ttp) REVERT: e 9 TYR cc_start: 0.7529 (m-80) cc_final: 0.7278 (m-80) REVERT: o 20 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6912 (tt0) REVERT: p 44 ILE cc_start: 0.8346 (mm) cc_final: 0.8064 (mt) REVERT: q 24 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7950 (mm) REVERT: u 1 MET cc_start: 0.4696 (tpp) cc_final: 0.1866 (tmm) REVERT: u 26 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7941 (tt) REVERT: v 32 SER cc_start: 0.8447 (t) cc_final: 0.8127 (m) REVERT: v 43 TYR cc_start: 0.7847 (t80) cc_final: 0.7445 (t80) REVERT: v 44 ILE cc_start: 0.7877 (mm) cc_final: 0.7544 (mt) REVERT: y 23 PHE cc_start: 0.4041 (OUTLIER) cc_final: 0.3745 (t80) REVERT: z 46 ARG cc_start: 0.4685 (tmt170) cc_final: 0.3706 (mpt180) REVERT: 5 23 PHE cc_start: 0.3213 (OUTLIER) cc_final: 0.2392 (t80) REVERT: 6 45 GLU cc_start: 0.5725 (mp0) cc_final: 0.5399 (mp0) outliers start: 74 outliers final: 54 residues processed: 584 average time/residue: 0.2176 time to fit residues: 213.7013 Evaluate side-chains 596 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 534 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 196 SER Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 138 MET Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain l residue 220 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 80 SER Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain o residue 20 GLN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain ab residue 25 MET Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 122 optimal weight: 5.9990 chunk 265 optimal weight: 0.4980 chunk 166 optimal weight: 1.9990 chunk 253 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 338 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 52 ASN l 199 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 39 HIS ** x 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN c 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.178858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.145630 restraints weight = 45956.291| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.27 r_work: 0.3173 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.349 37911 Z= 0.225 Angle : 0.666 12.900 52075 Z= 0.276 Chirality : 0.038 0.318 5131 Planarity : 0.003 0.036 6387 Dihedral : 14.764 139.625 6638 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.21 % Allowed : 16.26 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.14), residues: 3704 helix: 2.54 (0.10), residues: 2492 sheet: 0.00 (0.62), residues: 88 loop : -0.22 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l 109 TYR 0.020 0.001 TYR 0 24 PHE 0.033 0.001 PHE L 216 TRP 0.029 0.001 TRP x 48 HIS 0.011 0.001 HIS n 21 Details of bonding type rmsd covalent geometry : bond 0.00316 (37888) covalent geometry : angle 0.66603 (52075) hydrogen bonds : bond 0.04865 ( 2118) hydrogen bonds : angle 3.73173 ( 5994) Misc. bond : bond 0.07284 ( 23) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 529 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: L 216 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5867 (t80) REVERT: M 25 ASN cc_start: 0.4991 (t0) cc_final: 0.4568 (m-40) REVERT: M 165 PRO cc_start: 0.7642 (Cg_exo) cc_final: 0.7310 (Cg_endo) REVERT: M 216 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7899 (t80) REVERT: H 7 PHE cc_start: 0.8047 (p90) cc_final: 0.7650 (p90) REVERT: H 46 ASP cc_start: 0.5966 (p0) cc_final: 0.5170 (p0) REVERT: H 70 ARG cc_start: 0.5957 (mmt90) cc_final: 0.5379 (mmm160) REVERT: H 117 ARG cc_start: 0.6879 (mmm-85) cc_final: 0.6557 (mmm160) REVERT: H 118 ARG cc_start: 0.5205 (mtt180) cc_final: 0.3720 (mmm160) REVERT: H 206 ASN cc_start: 0.7960 (t0) cc_final: 0.7650 (t0) REVERT: H 255 MET cc_start: 0.5186 (mmt) cc_final: 0.4715 (ttt) REVERT: A 50 LYS cc_start: 0.7509 (tttt) cc_final: 0.6934 (ttmm) REVERT: A 52 ASN cc_start: 0.6969 (t0) cc_final: 0.6639 (t0) REVERT: D 33 LEU cc_start: 0.8391 (mt) cc_final: 0.7895 (mp) REVERT: F 8 TRP cc_start: 0.6106 (m100) cc_final: 0.5871 (m100) REVERT: G 18 GLN cc_start: 0.6431 (pt0) cc_final: 0.6095 (pt0) REVERT: G 44 ILE cc_start: 0.7221 (mm) cc_final: 0.6996 (mm) REVERT: N 25 MET cc_start: 0.5023 (mpp) cc_final: 0.3795 (mpp) REVERT: O 30 MET cc_start: 0.3439 (mmt) cc_final: 0.2966 (mmm) REVERT: 7 10 ILE cc_start: 0.7125 (mm) cc_final: 0.6900 (mt) REVERT: C 20 ARG cc_start: 0.7632 (ttm170) cc_final: 0.6157 (tmt170) REVERT: C 28 MET cc_start: 0.7869 (ttt) cc_final: 0.7494 (ttt) REVERT: l 82 LYS cc_start: 0.8794 (mttp) cc_final: 0.8490 (mtmt) REVERT: l 202 LYS cc_start: 0.8262 (tttt) cc_final: 0.8020 (ptmt) REVERT: l 213 ASP cc_start: 0.8800 (m-30) cc_final: 0.8557 (m-30) REVERT: l 216 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7870 (t80) REVERT: h 218 THR cc_start: 0.8132 (p) cc_final: 0.7777 (t) REVERT: h 255 MET cc_start: 0.3529 (mmt) cc_final: 0.2774 (ttp) REVERT: e 9 TYR cc_start: 0.7579 (m-80) cc_final: 0.7360 (m-80) REVERT: g 12 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6267 (mp) REVERT: n 34 VAL cc_start: 0.8239 (t) cc_final: 0.8032 (t) REVERT: p 44 ILE cc_start: 0.8381 (mm) cc_final: 0.8101 (mt) REVERT: q 24 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7885 (mm) REVERT: q 47 SER cc_start: 0.8352 (m) cc_final: 0.7889 (p) REVERT: u 1 MET cc_start: 0.4819 (tpp) cc_final: 0.1965 (tmm) REVERT: u 26 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7969 (tp) REVERT: v 43 TYR cc_start: 0.7848 (t80) cc_final: 0.7535 (t80) REVERT: v 44 ILE cc_start: 0.7972 (mm) cc_final: 0.7646 (mt) REVERT: y 23 PHE cc_start: 0.3952 (OUTLIER) cc_final: 0.3694 (t80) REVERT: z 46 ARG cc_start: 0.4730 (tmt170) cc_final: 0.3710 (mpt180) REVERT: 5 23 PHE cc_start: 0.3157 (OUTLIER) cc_final: 0.2397 (t80) REVERT: 6 45 GLU cc_start: 0.5890 (mp0) cc_final: 0.5503 (mp0) outliers start: 70 outliers final: 52 residues processed: 565 average time/residue: 0.2133 time to fit residues: 201.6841 Evaluate side-chains 583 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 523 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 196 SER Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 138 MET Chi-restraints excluded: chain l residue 216 PHE Chi-restraints excluded: chain l residue 220 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 80 SER Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 251 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 351 optimal weight: 3.9990 chunk 320 optimal weight: 9.9990 chunk 332 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 217 optimal weight: 0.2980 chunk 218 optimal weight: 0.0000 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 52 ASN 0 18 GLN l 199 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN ** v 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN c 66 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.177079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.143716 restraints weight = 45767.963| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.32 r_work: 0.3155 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 37911 Z= 0.157 Angle : 0.702 13.105 52075 Z= 0.291 Chirality : 0.040 0.416 5131 Planarity : 0.004 0.036 6387 Dihedral : 14.901 142.674 6638 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.34 % Allowed : 16.04 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.14), residues: 3704 helix: 2.46 (0.10), residues: 2472 sheet: -0.09 (0.61), residues: 88 loop : -0.17 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG l 109 TYR 0.019 0.001 TYR 0 24 PHE 0.033 0.001 PHE L 216 TRP 0.028 0.001 TRP x 48 HIS 0.012 0.001 HIS n 21 Details of bonding type rmsd covalent geometry : bond 0.00373 (37888) covalent geometry : angle 0.70176 (52075) hydrogen bonds : bond 0.05199 ( 2118) hydrogen bonds : angle 3.80206 ( 5994) Misc. bond : bond 0.00204 ( 23) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8160.62 seconds wall clock time: 140 minutes 57.88 seconds (8457.88 seconds total)