Starting phenix.real_space_refine on Thu Dec 26 17:09:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vot_32059/12_2024/7vot_32059.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vot_32059/12_2024/7vot_32059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vot_32059/12_2024/7vot_32059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vot_32059/12_2024/7vot_32059.map" model { file = "/net/cci-nas-00/data/ceres_data/7vot_32059/12_2024/7vot_32059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vot_32059/12_2024/7vot_32059.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 26 5.49 5 Mg 64 5.21 5 S 176 5.16 5 C 31648 2.51 5 N 6276 2.21 5 O 6792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44984 Number of models: 1 Model: "" Number of chains: 128 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: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "H" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1955 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 234} Chain: "A" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} 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: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "K" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} 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: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "R" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "V" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "W" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "3" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "Z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "2" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 328 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "7" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} 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: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "X" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "Y" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 375 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} 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: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "h" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1955 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 234} Chain: "a" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "b" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "d" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "e" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "f" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "g" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} 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: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "k" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "n" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} 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: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "r" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "s" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "t" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "u" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "v" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "w" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "c" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "5" 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: "z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "b1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "4" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 328 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "6" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "b8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "b9" 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: "b0" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "x" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "y" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 375 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "L" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 412 Unusual residues: {'BCL': 3, 'BPB': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "M" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'BCL': 1, 'BPB': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 32 Chain: "H" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 69 Chain: "A" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 220 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "B" 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: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "J" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 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: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "9" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 412 Unusual residues: {'BCL': 3, 'BPB': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "m" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'BCL': 1, 'BPB': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 32 Chain: "h" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 69 Chain: "a" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 220 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "b" 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: "d" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "i" 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: "j" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 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: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "v" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "w" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "5" 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: "z" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "b1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "b8" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "b9" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "b0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 25.82, per 1000 atoms: 0.57 Number of scatterers: 44984 At special positions: 0 Unit cell: (215.28, 140.4, 104, 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 176 16.00 P 26 15.00 Mg 64 11.99 O 6792 8.00 N 6276 7.00 C 31648 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=64, symmetry=0 Number of additional bonds: simple=64, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.61 Conformation dependent library (CDL) restraints added in 4.8 seconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8540 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 14 sheets defined 74.4% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 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 79 through 82 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.638A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU L 131 " --> pdb=" O ALA L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 Processing helix chain 'L' and resid 151 through 164 removed outlier: 3.734A pdb=" N ASP L 155 " --> pdb=" O TRP L 151 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 169 removed outlier: 5.947A pdb=" N HIS L 168 " --> pdb=" O GLY L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 Processing helix chain 'L' and resid 225 through 250 removed outlier: 3.627A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 263 removed outlier: 3.631A pdb=" N TRP L 262 " --> pdb=" O GLN L 258 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 258 through 263' Processing helix chain 'L' and resid 263 through 268 removed outlier: 3.902A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 43 removed outlier: 4.321A pdb=" N PHE M 42 " --> pdb=" O LEU M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 112 through 141 Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.663A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU M 156 " --> pdb=" O SER M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.509A pdb=" N GLU M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.622A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) 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: 3.620A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 290 removed outlier: 3.605A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE M 282 " --> pdb=" O LEU M 278 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER M 287 " --> pdb=" O GLY M 283 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY M 288 " --> pdb=" O ILE M 284 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR M 289 " --> pdb=" O LEU M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 300 Processing helix chain 'H' and resid 12 through 35 Processing helix chain 'H' and resid 36 through 38 No H-bonds generated for 'chain 'H' and resid 36 through 38' Processing helix chain 'H' and resid 67 through 70 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.917A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 removed outlier: 3.978A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 248 Processing helix chain 'H' and resid 250 through 256 Processing helix chain 'A' and resid 3 through 5 No H-bonds generated for 'chain 'A' and resid 3 through 5' Processing helix chain 'A' and resid 6 through 11 removed outlier: 3.549A pdb=" N ILE A 10 " --> pdb=" O LYS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.598A pdb=" N THR A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.580A pdb=" N ALA A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 46 Processing helix chain 'D' and resid 1 through 5 removed outlier: 4.202A pdb=" N TYR D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 removed outlier: 3.501A pdb=" N ILE D 10 " --> pdb=" O LYS D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 38 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 5 removed outlier: 3.874A pdb=" N TYR F 5 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 11 Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'G' and resid 13 through 46 Processing helix chain 'I' and resid 3 through 5 No H-bonds generated for 'chain 'I' and resid 3 through 5' Processing helix chain 'I' and resid 6 through 11 removed outlier: 3.822A pdb=" N ILE I 10 " --> pdb=" O LYS I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 38 Processing helix chain 'I' and resid 42 through 52 Processing helix chain 'J' and resid 13 through 46 Processing helix chain 'K' and resid 3 through 5 No H-bonds generated for 'chain 'K' and resid 3 through 5' Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 12 through 38 Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'N' and resid 13 through 46 Processing helix chain 'O' and resid 3 through 5 No H-bonds generated for 'chain 'O' and resid 3 through 5' Processing helix chain 'O' and resid 6 through 11 Processing helix chain 'O' and resid 12 through 38 removed outlier: 3.608A 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: 3.562A pdb=" N PHE Q 4 " --> pdb=" O MET Q 1 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR Q 5 " --> pdb=" O SER Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 51 removed outlier: 4.100A pdb=" N SER Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 46 Processing helix chain 'S' and resid 3 through 10 Processing helix chain 'S' and resid 12 through 38 Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 13 through 46 Processing helix chain 'U' and resid 3 through 5 No H-bonds generated for 'chain 'U' and resid 3 through 5' Processing helix chain 'U' and resid 6 through 11 removed outlier: 3.587A pdb=" N ILE U 10 " --> pdb=" O LYS U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 12 through 38 Processing helix chain 'U' and resid 42 through 51 Processing helix chain 'V' and resid 13 through 46 Processing helix chain 'W' and resid 3 through 10 Processing helix chain 'W' and resid 12 through 38 Processing helix chain 'W' and resid 42 through 52 Processing helix chain 'C' and resid 13 through 46 Processing helix chain '3' and resid 1 through 5 removed outlier: 3.979A pdb=" N PHE 3 4 " --> pdb=" O MET 3 1 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR 3 5 " --> pdb=" O SER 3 2 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 1 through 5' Processing helix chain '3' and resid 6 through 11 removed outlier: 3.965A pdb=" N ILE 3 10 " --> pdb=" O LYS 3 6 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 38 Processing helix chain '3' and resid 42 through 51 Processing helix chain 'Z' and resid 13 through 46 Processing helix chain '1' and resid 5 through 11 removed outlier: 3.752A pdb=" N MET 1 9 " --> pdb=" O TYR 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 38 Processing helix chain '1' and resid 42 through 51 Processing helix chain '2' and resid 13 through 46 Processing helix chain '7' and resid 3 through 10 Processing helix chain '7' and resid 12 through 38 Processing helix chain '7' and resid 42 through 47 removed outlier: 3.551A pdb=" N SER 7 47 " --> pdb=" O TRP 7 43 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 46 Processing helix chain '9' and resid 3 through 5 No H-bonds generated for 'chain '9' and resid 3 through 5' Processing helix chain '9' and resid 6 through 11 Processing helix chain '9' and resid 12 through 38 Processing helix chain '9' and resid 42 through 51 Processing helix chain '0' and resid 13 through 46 Processing helix chain 'X' and resid 18 through 55 Processing helix chain 'Y' and resid 5 through 29 Processing helix chain 'Y' and resid 31 through 48 removed outlier: 3.971A pdb=" N GLY Y 35 " --> pdb=" O HIS Y 31 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 10 Processing helix chain 'l' and resid 31 through 57 Processing helix chain 'l' and resid 70 through 74 Processing helix chain 'l' and resid 79 through 82 Processing helix chain 'l' and resid 83 through 112 Processing helix chain 'l' and resid 115 through 133 removed outlier: 3.638A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU l 131 " --> pdb=" O ALA l 127 " (cutoff:3.500A) Processing helix chain 'l' and resid 133 through 140 Processing helix chain 'l' and resid 141 through 145 Processing helix chain 'l' and resid 151 through 164 removed outlier: 3.735A pdb=" N ASP l 155 " --> pdb=" O TRP l 151 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 165 through 169 removed outlier: 5.947A pdb=" N HIS l 168 " --> pdb=" O GLY l 165 " (cutoff:3.500A) Processing helix chain 'l' and resid 170 through 199 Processing helix chain 'l' and resid 208 through 221 Processing helix chain 'l' and resid 225 through 250 removed outlier: 3.627A pdb=" N HIS l 230 " --> pdb=" O THR l 226 " (cutoff:3.500A) Processing helix chain 'l' and resid 258 through 263 removed outlier: 3.631A pdb=" N TRP l 262 " --> pdb=" O GLN l 258 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP l 263 " --> pdb=" O TRP l 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 258 through 263' Processing helix chain 'l' and resid 263 through 268 removed outlier: 3.903A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 43 removed outlier: 4.322A pdb=" N PHE m 42 " --> pdb=" O LEU m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 53 through 78 Processing helix chain 'm' and resid 81 through 88 Processing helix chain 'm' and resid 98 through 102 Processing helix chain 'm' and resid 112 through 141 Processing helix chain 'm' and resid 144 through 162 removed outlier: 3.662A pdb=" N ALA m 153 " --> pdb=" O ALA m 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU m 156 " --> pdb=" O SER m 152 " (cutoff:3.500A) Processing helix chain 'm' and resid 162 through 169 Processing helix chain 'm' and resid 170 through 174 removed outlier: 3.509A pdb=" N GLU m 173 " --> pdb=" O SER m 170 " (cutoff:3.500A) Processing helix chain 'm' and resid 178 through 193 removed outlier: 3.622A pdb=" N LEU m 183 " --> pdb=" O ILE m 179 " (cutoff:3.500A) 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: 3.620A pdb=" N TRP m 252 " --> pdb=" O ALA m 248 " (cutoff:3.500A) Processing helix chain 'm' and resid 263 through 290 removed outlier: 3.604A pdb=" N ARG m 267 " --> pdb=" O GLU m 263 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE m 282 " --> pdb=" O LEU m 278 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER m 287 " --> pdb=" O GLY m 283 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY m 288 " --> pdb=" O ILE m 284 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR m 289 " --> pdb=" O LEU m 285 " (cutoff:3.500A) Processing helix chain 'm' and resid 293 through 300 Processing helix chain 'h' and resid 12 through 35 Processing helix chain 'h' and resid 36 through 38 No H-bonds generated for 'chain 'h' and resid 36 through 38' Processing helix chain 'h' and resid 67 through 70 Processing helix chain 'h' and resid 103 through 108 Processing helix chain 'h' and resid 109 through 113 Processing helix chain 'h' and resid 194 through 196 No H-bonds generated for 'chain 'h' and resid 194 through 196' Processing helix chain 'h' and resid 209 through 216 removed outlier: 3.917A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) Processing helix chain 'h' and resid 226 through 244 removed outlier: 3.977A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 245 through 248 Processing helix chain 'h' and resid 250 through 256 Processing helix chain 'a' and resid 3 through 5 No H-bonds generated for 'chain 'a' and resid 3 through 5' Processing helix chain 'a' and resid 6 through 11 removed outlier: 3.549A pdb=" N ILE a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 38 removed outlier: 3.598A pdb=" N THR a 38 " --> pdb=" O ILE a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 51 removed outlier: 3.580A pdb=" N ALA a 48 " --> pdb=" O LEU a 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 46 Processing helix chain 'd' and resid 1 through 5 removed outlier: 4.202A pdb=" N TYR d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 11 removed outlier: 3.501A pdb=" N ILE d 10 " --> pdb=" O LYS d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 38 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 5 removed outlier: 3.874A pdb=" N TYR f 5 " --> pdb=" O SER f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 11 Processing helix chain 'f' and resid 12 through 38 Processing helix chain 'f' and resid 42 through 51 Processing helix chain 'g' and resid 13 through 46 Processing helix chain 'i' and resid 3 through 10 Processing helix chain 'i' and resid 12 through 38 Processing helix chain 'i' and resid 42 through 52 Processing helix chain 'j' and resid 13 through 46 Processing helix chain 'k' and resid 3 through 5 No H-bonds generated for 'chain 'k' and resid 3 through 5' Processing helix chain 'k' and resid 6 through 11 Processing helix chain 'k' and resid 12 through 38 Processing helix chain 'k' and resid 42 through 51 Processing helix chain 'n' and resid 13 through 46 Processing helix chain 'o' and resid 3 through 5 No H-bonds generated for 'chain 'o' and resid 3 through 5' Processing helix chain 'o' and resid 6 through 11 Processing helix chain 'o' and resid 12 through 38 removed outlier: 3.609A 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: 3.562A pdb=" N PHE q 4 " --> pdb=" O MET q 1 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR q 5 " --> pdb=" O SER q 2 " (cutoff:3.500A) Processing helix chain 'q' and resid 12 through 38 Processing helix chain 'q' and resid 42 through 51 removed outlier: 4.099A pdb=" N SER q 47 " --> pdb=" O TRP q 43 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA q 48 " --> pdb=" O LEU q 44 " (cutoff:3.500A) Processing helix chain 'r' and resid 13 through 46 Processing helix chain 's' and resid 3 through 10 Processing helix chain 's' and resid 12 through 38 Processing helix chain 's' and resid 42 through 51 Processing helix chain 't' and resid 13 through 46 Processing helix chain 'u' and resid 3 through 5 No H-bonds generated for 'chain 'u' and resid 3 through 5' Processing helix chain 'u' and resid 6 through 11 removed outlier: 3.587A pdb=" N ILE u 10 " --> pdb=" O LYS u 6 " (cutoff:3.500A) Processing helix chain 'u' and resid 12 through 38 Processing helix chain 'u' and resid 42 through 51 Processing helix chain 'v' and resid 13 through 46 Processing helix chain 'w' and resid 3 through 10 Processing helix chain 'w' and resid 12 through 38 Processing helix chain 'w' and resid 42 through 52 Processing helix chain 'c' and resid 13 through 46 Processing helix chain '5' and resid 1 through 5 removed outlier: 3.978A pdb=" N PHE 5 4 " --> pdb=" O MET 5 1 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR 5 5 " --> pdb=" O SER 5 2 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 1 through 5' Processing helix chain '5' and resid 6 through 11 removed outlier: 3.965A pdb=" N ILE 5 10 " --> pdb=" O LYS 5 6 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 38 Processing helix chain '5' and resid 42 through 51 Processing helix chain 'z' and resid 13 through 46 Processing helix chain 'b1' and resid 5 through 11 removed outlier: 3.753A pdb=" N METb1 9 " --> pdb=" O TYRb1 5 " (cutoff:3.500A) Processing helix chain 'b1' and resid 12 through 38 Processing helix chain 'b1' and resid 42 through 51 Processing helix chain '4' and resid 13 through 46 Processing helix chain '6' and resid 3 through 10 Processing helix chain '6' and resid 12 through 38 Processing helix chain '6' and resid 42 through 47 removed outlier: 3.551A pdb=" N SER 6 47 " --> pdb=" O TRP 6 43 " (cutoff:3.500A) Processing helix chain 'b8' and resid 13 through 46 Processing helix chain 'b9' and resid 3 through 5 No H-bonds generated for 'chain 'b9' and resid 3 through 5' Processing helix chain 'b9' and resid 6 through 11 Processing helix chain 'b9' and resid 12 through 38 Processing helix chain 'b9' and resid 42 through 51 Processing helix chain 'b0' and resid 13 through 46 Processing helix chain 'x' and resid 18 through 55 Processing helix chain 'y' and resid 5 through 29 Processing helix chain 'y' and resid 31 through 48 removed outlier: 3.970A pdb=" N GLY y 35 " --> pdb=" O HIS y 31 " (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 12 removed outlier: 6.506A pdb=" N GLN M 11 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.604A pdb=" N PHE H 7 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 62 through 65 Processing sheet with id=AA5, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA6, first strand: chain 'H' and resid 131 through 133 removed outlier: 5.707A pdb=" N VAL H 164 " --> pdb=" O GLU H 182 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLU H 182 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP H 170 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA H 176 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.789A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'l' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'm' and resid 11 through 12 removed outlier: 6.506A pdb=" N GLN m 11 " --> pdb=" O SER h 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'h' and resid 5 through 7 removed outlier: 3.604A pdb=" N PHE h 7 " --> pdb=" O PHE h 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'h' and resid 62 through 65 Processing sheet with id=AB3, first strand: chain 'h' and resid 87 through 89 Processing sheet with id=AB4, first strand: chain 'h' and resid 131 through 133 removed outlier: 5.707A pdb=" N VAL h 164 " --> pdb=" O GLU h 182 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLU h 182 " --> pdb=" O VAL h 164 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ASP h 170 " --> pdb=" O ALA h 176 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA h 176 " --> pdb=" O ASP h 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 131 through 133 removed outlier: 3.788A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 2568 hydrogen bonds defined for protein. 7407 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: 15.34 Time building geometry restraints manager: 14.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 12008 1.35 - 1.56: 34042 1.56 - 1.76: 52 1.76 - 1.97: 342 1.97 - 2.17: 256 Bond restraints: 46700 Sorted by residual: bond pdb=" C3C BPB L 303 " pdb=" CAC BPB L 303 " ideal model delta sigma weight residual 1.334 1.551 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C3C BPB l 303 " pdb=" CAC BPB l 303 " ideal model delta sigma weight residual 1.334 1.551 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C3C BPB M 403 " pdb=" CAC BPB M 403 " ideal model delta sigma weight residual 1.334 1.546 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3C BPB m 403 " pdb=" CAC BPB m 403 " ideal model delta sigma weight residual 1.334 1.546 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" OB3 CDL m 406 " pdb=" PB2 CDL m 406 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.00e-02 1.00e+04 5.21e+01 ... (remaining 46695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 63326 3.25 - 6.49: 739 6.49 - 9.74: 49 9.74 - 12.99: 12 12.99 - 16.24: 12 Bond angle restraints: 64138 Sorted by residual: angle pdb=" C51 CDL m 406 " pdb=" CB5 CDL m 406 " pdb=" OB6 CDL m 406 " ideal model delta sigma weight residual 111.33 120.72 -9.39 1.32e+00 5.72e-01 5.05e+01 angle pdb=" C51 CDL M 406 " pdb=" CB5 CDL M 406 " pdb=" OB6 CDL M 406 " ideal model delta sigma weight residual 111.33 120.72 -9.39 1.32e+00 5.72e-01 5.04e+01 angle pdb=" C11 CDL h 303 " pdb=" CA5 CDL h 303 " pdb=" OA6 CDL h 303 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.51e+01 angle pdb=" C11 CDL H 303 " pdb=" CA5 CDL H 303 " pdb=" OA6 CDL H 303 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.51e+01 angle pdb=" C11 CDL m 406 " pdb=" CA5 CDL m 406 " pdb=" OA6 CDL m 406 " ideal model delta sigma weight residual 111.33 120.07 -8.74 1.32e+00 5.72e-01 4.37e+01 ... (remaining 64133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 24388 35.97 - 71.94: 550 71.94 - 107.92: 70 107.92 - 143.89: 10 143.89 - 179.86: 4 Dihedral angle restraints: 25022 sinusoidal: 11736 harmonic: 13286 Sorted by residual: dihedral pdb=" C1 BCL G 101 " pdb=" C2 BCL G 101 " pdb=" C3 BCL G 101 " pdb=" C5 BCL G 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.14 179.86 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL g 101 " pdb=" C2 BCL g 101 " pdb=" C3 BCL g 101 " pdb=" C5 BCL g 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.19 179.81 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 2 101 " pdb=" C2 BCL 2 101 " pdb=" C3 BCL 2 101 " pdb=" C5 BCL 2 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.54 -179.46 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 25019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4686 0.042 - 0.084: 1306 0.084 - 0.126: 203 0.126 - 0.168: 12 0.168 - 0.210: 9 Chirality restraints: 6216 Sorted by residual: chirality pdb=" C2C BPB m 403 " pdb=" C1C BPB m 403 " pdb=" C3C BPB m 403 " pdb=" CMC BPB m 403 " both_signs ideal model delta sigma weight residual False -2.78 -2.57 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C2C BPB M 403 " pdb=" C1C BPB M 403 " pdb=" C3C BPB M 403 " pdb=" CMC BPB M 403 " both_signs ideal model delta sigma weight residual False -2.78 -2.57 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG M 247 " pdb=" N ARG M 247 " pdb=" C ARG M 247 " pdb=" CB ARG M 247 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 6213 not shown) Planarity restraints: 7888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2C BPB L 303 " -0.381 2.00e-02 2.50e+03 5.00e-01 3.13e+03 pdb=" C3C BPB L 303 " 0.502 2.00e-02 2.50e+03 pdb=" C4C BPB L 303 " -0.207 2.00e-02 2.50e+03 pdb=" CAC BPB L 303 " 0.678 2.00e-02 2.50e+03 pdb=" CBC BPB L 303 " -0.591 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB l 303 " 0.382 2.00e-02 2.50e+03 5.00e-01 3.12e+03 pdb=" C3C BPB l 303 " -0.502 2.00e-02 2.50e+03 pdb=" C4C BPB l 303 " 0.207 2.00e-02 2.50e+03 pdb=" CAC BPB l 303 " -0.678 2.00e-02 2.50e+03 pdb=" CBC BPB l 303 " 0.591 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB M 403 " -0.007 2.00e-02 2.50e+03 2.37e-01 7.03e+02 pdb=" C3C BPB M 403 " -0.333 2.00e-02 2.50e+03 pdb=" C4C BPB M 403 " 0.140 2.00e-02 2.50e+03 pdb=" CAC BPB M 403 " 0.356 2.00e-02 2.50e+03 pdb=" CBC BPB M 403 " -0.156 2.00e-02 2.50e+03 ... (remaining 7885 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 959 2.70 - 3.25: 42141 3.25 - 3.80: 77296 3.80 - 4.35: 105442 4.35 - 4.90: 171473 Nonbonded interactions: 397311 Sorted by model distance: nonbonded pdb=" NE2 HIS l 190 " pdb="FE FE2 m 401 " model vdw 2.147 3.080 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE2 M 401 " model vdw 2.147 3.080 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE2 M 401 " model vdw 2.150 3.000 nonbonded pdb=" OE1 GLU m 234 " pdb="FE FE2 m 401 " model vdw 2.151 3.000 nonbonded pdb=" NE2 HIS M 219 " pdb="FE FE2 M 401 " model vdw 2.158 3.080 ... (remaining 397306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 10 through 49) selection = (chain '2' and resid 10 through 49) selection = (chain '4' and resid 10 through 49) selection = (chain '8' and resid 10 through 49) selection = (chain 'B' and resid 10 through 49) selection = (chain 'C' and resid 10 through 49) selection = (chain 'E' and resid 10 through 49) selection = (chain 'G' and resid 10 through 49) selection = (chain 'J' and resid 10 through 49) selection = (chain 'N' and resid 10 through 49) selection = (chain 'P' and resid 10 through 49) selection = (chain 'R' and resid 10 through 49) selection = (chain 'T' and resid 10 through 49) selection = (chain 'V' and resid 10 through 49) selection = (chain 'Z' and resid 10 through 49) selection = (chain 'b' and resid 10 through 49) selection = (chain 'b0' and resid 10 through 49) selection = (chain 'b8' and resid 10 through 49) selection = (chain 'c' and resid 10 through 49) selection = (chain 'e' and resid 10 through 49) selection = (chain 'g' and resid 10 through 49) selection = (chain 'j' and resid 10 through 49) selection = (chain 'n' and resid 10 through 49) selection = (chain 'p' and resid 10 through 49) selection = (chain 'r' and resid 10 through 49) selection = (chain 't' and resid 10 through 49) selection = (chain 'v' and resid 10 through 49) selection = (chain 'z' and resid 10 through 49) } ncs_group { reference = (chain '1' and resid 2 through 48) selection = (chain '3' and resid 2 through 48) selection = (chain '5' and resid 2 through 48) selection = (chain '6' and resid 2 through 48) selection = (chain '7' and resid 2 through 48) selection = (chain '9' and resid 2 through 48) selection = (chain 'A' and resid 2 through 48) selection = (chain 'D' and resid 2 through 48) selection = (chain 'F' and resid 2 through 48) selection = (chain 'I' and resid 2 through 48) selection = (chain 'K' and resid 2 through 48) selection = (chain 'O' and resid 2 through 48) selection = (chain 'Q' and resid 2 through 48) selection = (chain 'S' and resid 2 through 48) selection = (chain 'U' and resid 2 through 48) selection = (chain 'W' and resid 2 through 48) selection = (chain 'a' and resid 2 through 48) selection = (chain 'b1' and resid 2 through 48) selection = (chain 'b9' and resid 2 through 48) selection = (chain 'd' and resid 2 through 48) selection = (chain 'f' and resid 2 through 48) selection = (chain 'i' and resid 2 through 48) selection = (chain 'k' and resid 2 through 48) selection = (chain 'o' and resid 2 through 48) selection = (chain 'q' and resid 2 through 48) selection = (chain 's' and resid 2 through 48) selection = (chain 'u' and resid 2 through 48) selection = (chain 'w' and resid 2 through 48) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'Y' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.630 Check model and map are aligned: 0.350 Set scattering table: 0.380 Process input model: 92.810 Find NCS groups from input model: 3.570 Set up NCS constraints: 0.270 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:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.006 0.217 46700 Z= 0.353 Angle : 0.796 16.237 64138 Z= 0.329 Chirality : 0.038 0.210 6216 Planarity : 0.009 0.500 7888 Dihedral : 15.277 179.859 16482 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.37 % Allowed : 3.31 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.12), residues: 4462 helix: 2.48 (0.09), residues: 2912 sheet: -0.44 (0.84), residues: 48 loop : 0.42 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 263 HIS 0.009 0.001 HIS l 153 PHE 0.016 0.001 PHE l 216 TYR 0.013 0.001 TYR a 41 ARG 0.003 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1153 time to evaluate : 4.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8669 (m) cc_final: 0.8312 (t) REVERT: M 23 ASP cc_start: 0.6976 (t0) cc_final: 0.6668 (t70) REVERT: M 236 GLU cc_start: 0.5951 (pt0) cc_final: 0.5665 (pt0) REVERT: H 19 SER cc_start: 0.9267 (p) cc_final: 0.9065 (p) REVERT: H 93 SER cc_start: 0.8088 (t) cc_final: 0.7877 (p) REVERT: H 128 HIS cc_start: 0.6873 (m90) cc_final: 0.6612 (m170) REVERT: H 170 ASP cc_start: 0.7118 (t0) cc_final: 0.6761 (t70) REVERT: H 184 LYS cc_start: 0.7216 (mmtp) cc_final: 0.6794 (ttmm) REVERT: H 230 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7753 (mt-10) REVERT: D 5 TYR cc_start: 0.8496 (p90) cc_final: 0.8163 (p90) REVERT: G 9 TYR cc_start: 0.7180 (m-10) cc_final: 0.6975 (m-80) REVERT: K 5 TYR cc_start: 0.7624 (p90) cc_final: 0.7416 (p90) REVERT: K 26 LEU cc_start: 0.8881 (mt) cc_final: 0.8635 (mm) REVERT: O 30 MET cc_start: 0.8060 (ttm) cc_final: 0.7654 (ttm) REVERT: S 3 LYS cc_start: 0.8725 (mttt) cc_final: 0.8488 (mmtm) REVERT: W 8 TRP cc_start: 0.9042 (m100) cc_final: 0.8630 (m100) REVERT: C 25 MET cc_start: 0.8214 (mmm) cc_final: 0.8009 (mmm) REVERT: X 17 THR cc_start: 0.6661 (m) cc_final: 0.6447 (t) REVERT: X 53 ARG cc_start: 0.6628 (mtt-85) cc_final: 0.5483 (ptm160) REVERT: l 48 LEU cc_start: 0.8851 (mt) cc_final: 0.8536 (mt) REVERT: l 52 SER cc_start: 0.8681 (t) cc_final: 0.8446 (m) REVERT: m 23 ASP cc_start: 0.7084 (t0) cc_final: 0.6841 (t70) REVERT: m 36 SER cc_start: 0.8613 (t) cc_final: 0.8393 (t) REVERT: m 233 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7217 (ttp-110) REVERT: m 246 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7851 (mt-10) REVERT: m 272 MET cc_start: 0.8399 (tpp) cc_final: 0.8172 (tpp) REVERT: h 173 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7279 (mp0) REVERT: a 44 LEU cc_start: 0.8996 (mt) cc_final: 0.8714 (mt) REVERT: d 5 TYR cc_start: 0.8493 (p90) cc_final: 0.8120 (p90) REVERT: f 15 ARG cc_start: 0.6707 (mmt90) cc_final: 0.6187 (mtp-110) REVERT: g 9 TYR cc_start: 0.7139 (m-10) cc_final: 0.6919 (m-80) REVERT: k 6 LYS cc_start: 0.8096 (tptt) cc_final: 0.7879 (tptm) REVERT: k 26 LEU cc_start: 0.8923 (mt) cc_final: 0.8644 (mm) REVERT: k 41 TYR cc_start: 0.7328 (m-80) cc_final: 0.7051 (m-80) REVERT: n 28 LEU cc_start: 0.9095 (tp) cc_final: 0.8876 (tp) REVERT: 5 5 TYR cc_start: 0.7992 (p90) cc_final: 0.7370 (p90) REVERT: 4 16 GLN cc_start: 0.7429 (mt0) cc_final: 0.7116 (mm110) REVERT: 6 14 ARG cc_start: 0.6966 (ptm160) cc_final: 0.6558 (ttp-110) REVERT: 6 30 MET cc_start: 0.8144 (ttm) cc_final: 0.7660 (ttm) REVERT: x 28 MET cc_start: 0.7010 (ttm) cc_final: 0.6728 (tpt) REVERT: x 53 ARG cc_start: 0.6363 (mtt-85) cc_final: 0.5348 (ptm160) REVERT: y 6 GLU cc_start: 0.6869 (tp30) cc_final: 0.6561 (tp30) outliers start: 14 outliers final: 10 residues processed: 1160 average time/residue: 1.2878 time to fit residues: 1917.3803 Evaluate side-chains 864 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 854 time to evaluate : 4.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain b1 residue 29 VAL Chi-restraints excluded: chain b0 residue 40 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 1.9990 chunk 330 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 341 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 395 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 199 ASN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN D 20 GLN I 20 GLN R 16 GLN V 18 GLN 3 20 GLN Z 18 GLN 7 20 GLN l 199 ASN h 194 GLN h 199 GLN i 20 GLN k 42 ASN k 52 ASN n 18 GLN q 52 ASN r 16 GLN ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 18 GLN z 16 GLN 6 20 GLN x 26 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 46700 Z= 0.416 Angle : 0.746 11.251 64138 Z= 0.324 Chirality : 0.042 0.169 6216 Planarity : 0.004 0.052 7888 Dihedral : 16.843 179.954 8473 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.83 % Allowed : 13.13 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.12), residues: 4462 helix: 2.07 (0.09), residues: 2922 sheet: -0.85 (0.77), residues: 48 loop : 0.29 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 48 HIS 0.012 0.002 HIS z 21 PHE 0.026 0.002 PHE O 17 TYR 0.020 0.002 TYR j 24 ARG 0.008 0.001 ARG H 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 962 time to evaluate : 4.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8742 (m) cc_final: 0.8321 (t) REVERT: M 23 ASP cc_start: 0.7266 (t0) cc_final: 0.7014 (t70) REVERT: H 79 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6761 (mt-10) REVERT: H 170 ASP cc_start: 0.7388 (t0) cc_final: 0.6862 (t70) REVERT: H 184 LYS cc_start: 0.7140 (mmtp) cc_final: 0.6686 (ttmm) REVERT: A 9 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7653 (mmm) REVERT: D 5 TYR cc_start: 0.8616 (p90) cc_final: 0.8320 (p90) REVERT: F 15 ARG cc_start: 0.6841 (mmt90) cc_final: 0.6341 (mtp-110) REVERT: G 9 TYR cc_start: 0.7283 (m-10) cc_final: 0.7056 (m-80) REVERT: I 3 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8018 (mtmm) REVERT: J 32 SER cc_start: 0.8818 (p) cc_final: 0.8600 (m) REVERT: K 3 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8227 (tmtp) REVERT: K 5 TYR cc_start: 0.8037 (p90) cc_final: 0.7793 (p90) REVERT: K 41 TYR cc_start: 0.7404 (m-80) cc_final: 0.6980 (m-80) REVERT: O 3 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7523 (tptp) REVERT: O 17 PHE cc_start: 0.8663 (m-80) cc_final: 0.8457 (m-80) REVERT: O 30 MET cc_start: 0.8261 (ttm) cc_final: 0.8042 (ttm) REVERT: Q 6 LYS cc_start: 0.8284 (tptm) cc_final: 0.8064 (tptm) REVERT: S 3 LYS cc_start: 0.8842 (mttt) cc_final: 0.8595 (mmtm) REVERT: U 15 ARG cc_start: 0.7890 (mmt90) cc_final: 0.7088 (mtm110) REVERT: W 41 TYR cc_start: 0.7299 (m-80) cc_final: 0.7048 (m-80) REVERT: 3 7 ILE cc_start: 0.8404 (tp) cc_final: 0.8161 (pt) REVERT: X 28 MET cc_start: 0.6485 (tmm) cc_final: 0.6236 (tmm) REVERT: X 53 ARG cc_start: 0.6663 (mtt-85) cc_final: 0.5494 (ptm160) REVERT: l 213 ASP cc_start: 0.7611 (m-30) cc_final: 0.7390 (m-30) REVERT: m 21 THR cc_start: 0.8718 (m) cc_final: 0.8299 (t) REVERT: m 23 ASP cc_start: 0.7079 (t0) cc_final: 0.6782 (t0) REVERT: m 184 ASP cc_start: 0.7649 (m-30) cc_final: 0.7400 (m-30) REVERT: m 233 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7121 (ttm110) REVERT: h 18 TYR cc_start: 0.8999 (m-80) cc_final: 0.8787 (m-80) REVERT: h 170 ASP cc_start: 0.7714 (t0) cc_final: 0.7117 (t70) REVERT: h 173 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7368 (mp0) REVERT: e 18 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8073 (mt0) REVERT: f 15 ARG cc_start: 0.6946 (mmt90) cc_final: 0.6428 (mtp-110) REVERT: i 3 LYS cc_start: 0.8390 (mtpm) cc_final: 0.8157 (mtmm) REVERT: i 5 TYR cc_start: 0.8257 (p90) cc_final: 0.7963 (p90) REVERT: j 32 SER cc_start: 0.8867 (p) cc_final: 0.8550 (m) REVERT: k 41 TYR cc_start: 0.7584 (m-80) cc_final: 0.7265 (m-80) REVERT: o 3 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7603 (mtpp) REVERT: q 45 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: s 46 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7842 (mp) REVERT: u 15 ARG cc_start: 0.7760 (mmt90) cc_final: 0.7448 (mtt90) REVERT: v 14 ASP cc_start: 0.7497 (t0) cc_final: 0.7187 (t0) REVERT: 5 5 TYR cc_start: 0.7967 (p90) cc_final: 0.7343 (p90) REVERT: z 43 TYR cc_start: 0.7202 (t80) cc_final: 0.6955 (t80) REVERT: b1 6 LYS cc_start: 0.7058 (mmtt) cc_final: 0.6844 (mmtp) REVERT: x 53 ARG cc_start: 0.6449 (mtt-85) cc_final: 0.5521 (ptm160) REVERT: y 10 ARG cc_start: 0.7736 (tpt170) cc_final: 0.7450 (tpt170) REVERT: y 36 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8498 (tp) outliers start: 146 outliers final: 51 residues processed: 1023 average time/residue: 1.1788 time to fit residues: 1561.4602 Evaluate side-chains 920 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 861 time to evaluate : 4.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 46 ILE Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 159 VAL Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain o residue 37 SER Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 45 GLU Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 46 ILE Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain z residue 42 VAL Chi-restraints excluded: chain b1 residue 20 GLN Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 4 residue 46 ARG Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b8 residue 40 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Chi-restraints excluded: chain y residue 36 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 220 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 329 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 396 optimal weight: 9.9990 chunk 428 optimal weight: 0.8980 chunk 353 optimal weight: 1.9990 chunk 393 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN I 20 GLN N 18 GLN ** W 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 GLN Z 18 GLN 7 20 GLN Y 51 ASN l 199 ASN h 35 ASN h 194 GLN k 52 ASN r 16 GLN v 16 GLN ** z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 18 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 46700 Z= 0.274 Angle : 0.653 11.388 64138 Z= 0.283 Chirality : 0.039 0.149 6216 Planarity : 0.004 0.042 7888 Dihedral : 16.409 179.969 8466 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.99 % Allowed : 15.86 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.12), residues: 4462 helix: 2.11 (0.09), residues: 2922 sheet: -0.93 (0.75), residues: 48 loop : 0.26 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 48 HIS 0.014 0.001 HIS Z 21 PHE 0.036 0.001 PHE o 17 TYR 0.017 0.002 TYR P 24 ARG 0.005 0.001 ARG M 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 945 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8583 (m) cc_final: 0.8141 (t) REVERT: M 23 ASP cc_start: 0.7228 (t0) cc_final: 0.7013 (t70) REVERT: H 184 LYS cc_start: 0.6970 (mmtp) cc_final: 0.6464 (ttmm) REVERT: D 5 TYR cc_start: 0.8707 (p90) cc_final: 0.8432 (p90) REVERT: E 18 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: F 1 MET cc_start: 0.7141 (mmm) cc_final: 0.6907 (mmm) REVERT: F 15 ARG cc_start: 0.6890 (mmt90) cc_final: 0.6397 (mtp-110) REVERT: I 5 TYR cc_start: 0.8324 (p90) cc_final: 0.8052 (p90) REVERT: K 5 TYR cc_start: 0.8148 (p90) cc_final: 0.7905 (p90) REVERT: O 3 LYS cc_start: 0.7811 (ttmm) cc_final: 0.7355 (tptt) REVERT: P 16 GLN cc_start: 0.7803 (mt0) cc_final: 0.7577 (mt0) REVERT: Q 6 LYS cc_start: 0.8413 (tptm) cc_final: 0.8143 (tptm) REVERT: S 3 LYS cc_start: 0.8859 (mttt) cc_final: 0.8616 (mmtm) REVERT: U 9 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7978 (mmm) REVERT: U 15 ARG cc_start: 0.7818 (mmt90) cc_final: 0.7185 (mtm110) REVERT: W 37 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8387 (p) REVERT: 3 7 ILE cc_start: 0.8394 (tp) cc_final: 0.8169 (pt) REVERT: 9 45 GLU cc_start: 0.7475 (tt0) cc_final: 0.7266 (tt0) REVERT: X 17 THR cc_start: 0.6781 (m) cc_final: 0.6230 (t) REVERT: X 28 MET cc_start: 0.6503 (tmm) cc_final: 0.6255 (tmm) REVERT: X 53 ARG cc_start: 0.6791 (mtt-85) cc_final: 0.5631 (ptm160) REVERT: l 20 ASN cc_start: 0.8105 (p0) cc_final: 0.7897 (p0) REVERT: m 21 THR cc_start: 0.8544 (m) cc_final: 0.8126 (t) REVERT: m 23 ASP cc_start: 0.7182 (t0) cc_final: 0.6891 (t0) REVERT: m 36 SER cc_start: 0.8684 (t) cc_final: 0.8448 (p) REVERT: m 122 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8289 (ttt) REVERT: m 233 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.6773 (ttm110) REVERT: h 170 ASP cc_start: 0.7700 (t0) cc_final: 0.7123 (t70) REVERT: h 173 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7387 (mp0) REVERT: e 18 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: f 3 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7854 (ttmt) REVERT: f 15 ARG cc_start: 0.6940 (mmt90) cc_final: 0.6464 (mtp-110) REVERT: i 5 TYR cc_start: 0.8249 (p90) cc_final: 0.7972 (p90) REVERT: j 32 SER cc_start: 0.8871 (p) cc_final: 0.8593 (m) REVERT: k 41 TYR cc_start: 0.7519 (m-80) cc_final: 0.7112 (m-80) REVERT: n 16 GLN cc_start: 0.7224 (mt0) cc_final: 0.6995 (mt0) REVERT: n 28 LEU cc_start: 0.9150 (tt) cc_final: 0.8939 (tp) REVERT: o 3 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7600 (mtpp) REVERT: p 10 THR cc_start: 0.6718 (OUTLIER) cc_final: 0.6478 (p) REVERT: p 13 THR cc_start: 0.7648 (m) cc_final: 0.7366 (p) REVERT: q 45 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: r 7 LEU cc_start: 0.5000 (OUTLIER) cc_final: 0.4729 (tp) REVERT: s 14 ARG cc_start: 0.8303 (mtm110) cc_final: 0.7720 (mtm180) REVERT: u 15 ARG cc_start: 0.7804 (mmt90) cc_final: 0.7457 (mtt90) REVERT: v 14 ASP cc_start: 0.7551 (t0) cc_final: 0.7175 (t0) REVERT: v 16 GLN cc_start: 0.8291 (mt0) cc_final: 0.8039 (mt0) REVERT: w 9 MET cc_start: 0.8384 (mtp) cc_final: 0.8160 (mmt) REVERT: w 37 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8486 (p) REVERT: c 9 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.7004 (m-10) REVERT: 5 5 TYR cc_start: 0.7856 (p90) cc_final: 0.7354 (p90) REVERT: z 43 TYR cc_start: 0.7198 (t80) cc_final: 0.6968 (t80) REVERT: b1 6 LYS cc_start: 0.7186 (mmtt) cc_final: 0.6939 (mmtp) REVERT: x 28 MET cc_start: 0.7457 (mtm) cc_final: 0.7202 (tmt) REVERT: x 53 ARG cc_start: 0.6458 (mtt-85) cc_final: 0.5404 (ptm160) REVERT: y 36 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8147 (tm) outliers start: 152 outliers final: 58 residues processed: 1014 average time/residue: 1.0923 time to fit residues: 1435.7764 Evaluate side-chains 944 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 874 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain U residue 9 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain 3 residue 27 LEU Chi-restraints excluded: chain 1 residue 20 GLN Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 122 MET Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain f residue 3 LYS Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain k residue 7 ILE Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 45 GLU Chi-restraints excluded: chain r residue 7 LEU Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Chi-restraints excluded: chain y residue 36 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 391 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 398 optimal weight: 3.9990 chunk 421 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 377 optimal weight: 0.2980 chunk 113 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN N 16 GLN Q 20 GLN W 20 GLN 3 20 GLN Z 18 GLN 7 20 GLN Y 51 ASN l 199 ASN h 35 ASN ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 194 GLN k 42 ASN k 52 ASN c 18 GLN b1 20 GLN 4 18 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 46700 Z= 0.215 Angle : 0.624 11.183 64138 Z= 0.272 Chirality : 0.038 0.137 6216 Planarity : 0.004 0.081 7888 Dihedral : 16.081 179.940 8466 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.55 % Allowed : 18.07 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.12), residues: 4462 helix: 2.28 (0.09), residues: 2904 sheet: -0.82 (0.75), residues: 48 loop : 0.26 (0.17), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP j 48 HIS 0.014 0.001 HIS z 21 PHE 0.038 0.001 PHE O 17 TYR 0.018 0.001 TYR W 41 ARG 0.005 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 969 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8585 (m) cc_final: 0.8055 (t) REVERT: M 23 ASP cc_start: 0.7167 (t0) cc_final: 0.6800 (t0) REVERT: M 122 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8252 (ttt) REVERT: H 184 LYS cc_start: 0.6935 (mmtp) cc_final: 0.6432 (ttmm) REVERT: D 5 TYR cc_start: 0.8695 (p90) cc_final: 0.8435 (p90) REVERT: E 18 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: F 15 ARG cc_start: 0.6796 (mmt90) cc_final: 0.6399 (mtp-110) REVERT: I 3 LYS cc_start: 0.8147 (mtpm) cc_final: 0.7768 (tppp) REVERT: I 5 TYR cc_start: 0.8340 (p90) cc_final: 0.8108 (p90) REVERT: I 39 PRO cc_start: 0.8820 (Cg_exo) cc_final: 0.8613 (Cg_endo) REVERT: J 28 LEU cc_start: 0.9177 (tt) cc_final: 0.8956 (tp) REVERT: K 5 TYR cc_start: 0.8101 (p90) cc_final: 0.7883 (p90) REVERT: O 3 LYS cc_start: 0.7928 (ttmm) cc_final: 0.7467 (tptt) REVERT: Q 6 LYS cc_start: 0.8359 (tptm) cc_final: 0.8126 (tppp) REVERT: S 3 LYS cc_start: 0.8861 (mttt) cc_final: 0.8643 (mmtm) REVERT: S 14 ARG cc_start: 0.7813 (mtm180) cc_final: 0.7572 (mtm180) REVERT: U 15 ARG cc_start: 0.7765 (mmt90) cc_final: 0.7156 (mtm110) REVERT: C 9 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7102 (m-10) REVERT: 1 26 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8568 (mp) REVERT: 2 15 GLU cc_start: 0.6307 (pm20) cc_final: 0.5927 (pm20) REVERT: 9 10 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8621 (mt) REVERT: 9 45 GLU cc_start: 0.7498 (tt0) cc_final: 0.7278 (tt0) REVERT: 0 16 GLN cc_start: 0.8505 (mt0) cc_final: 0.8274 (mt0) REVERT: X 17 THR cc_start: 0.6538 (m) cc_final: 0.6017 (t) REVERT: X 28 MET cc_start: 0.6544 (tmm) cc_final: 0.6240 (tmm) REVERT: X 53 ARG cc_start: 0.6664 (mtt-85) cc_final: 0.5492 (ptm160) REVERT: Y 6 GLU cc_start: 0.7002 (tp30) cc_final: 0.6668 (tp30) REVERT: Y 10 ARG cc_start: 0.7743 (tpt90) cc_final: 0.7440 (mtt-85) REVERT: m 21 THR cc_start: 0.8552 (m) cc_final: 0.8033 (t) REVERT: m 23 ASP cc_start: 0.7015 (t0) cc_final: 0.6682 (t0) REVERT: m 122 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8217 (ttt) REVERT: m 233 ARG cc_start: 0.7278 (mtm-85) cc_final: 0.6976 (mtm180) REVERT: h 173 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7573 (mp0) REVERT: h 226 THR cc_start: 0.8782 (p) cc_final: 0.8290 (t) REVERT: d 5 TYR cc_start: 0.8721 (p90) cc_final: 0.8409 (p90) REVERT: e 18 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: f 15 ARG cc_start: 0.6956 (mmt90) cc_final: 0.6524 (mtp-110) REVERT: i 3 LYS cc_start: 0.8383 (mtpm) cc_final: 0.7998 (tppp) REVERT: i 5 TYR cc_start: 0.8208 (p90) cc_final: 0.7859 (p90) REVERT: i 39 PRO cc_start: 0.8817 (Cg_exo) cc_final: 0.8604 (Cg_endo) REVERT: j 16 GLN cc_start: 0.7689 (mt0) cc_final: 0.7461 (tt0) REVERT: j 32 SER cc_start: 0.8785 (p) cc_final: 0.8583 (m) REVERT: k 6 LYS cc_start: 0.7797 (tptm) cc_final: 0.7384 (tptp) REVERT: n 16 GLN cc_start: 0.7205 (mt0) cc_final: 0.6982 (mt0) REVERT: o 3 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7718 (mtpp) REVERT: p 10 THR cc_start: 0.6492 (OUTLIER) cc_final: 0.6254 (p) REVERT: p 13 THR cc_start: 0.7536 (m) cc_final: 0.7271 (p) REVERT: q 45 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: r 7 LEU cc_start: 0.4751 (OUTLIER) cc_final: 0.4536 (tp) REVERT: s 14 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7695 (mtt90) REVERT: u 15 ARG cc_start: 0.7780 (mmt90) cc_final: 0.7489 (mtt90) REVERT: v 16 GLN cc_start: 0.8035 (mt0) cc_final: 0.7791 (mt0) REVERT: w 37 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8519 (p) REVERT: c 9 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.6896 (m-80) REVERT: z 43 TYR cc_start: 0.7167 (t80) cc_final: 0.6936 (t80) REVERT: b1 4 PHE cc_start: 0.6357 (OUTLIER) cc_final: 0.5813 (m-80) REVERT: b1 37 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8542 (p) REVERT: b9 10 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8587 (mt) REVERT: x 53 ARG cc_start: 0.6407 (mtt-85) cc_final: 0.5552 (ptm160) REVERT: y 36 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8139 (tm) outliers start: 135 outliers final: 42 residues processed: 1025 average time/residue: 1.0233 time to fit residues: 1361.3075 Evaluate side-chains 951 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 893 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain C residue 9 TYR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 3 residue 27 LEU Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain m residue 122 MET Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain k residue 7 ILE Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 45 GLU Chi-restraints excluded: chain r residue 7 LEU Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b8 residue 40 LEU Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 350 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 359 optimal weight: 1.9990 chunk 291 optimal weight: 0.0570 chunk 0 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 378 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN K 42 ASN N 16 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 18 GLN 7 20 GLN Y 51 ASN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 199 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN k 42 ASN ** t 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 20 GLN x 18 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 46700 Z= 0.313 Angle : 0.694 11.010 64138 Z= 0.299 Chirality : 0.040 0.195 6216 Planarity : 0.004 0.057 7888 Dihedral : 16.238 179.910 8464 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.99 % Allowed : 19.56 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.12), residues: 4462 helix: 2.13 (0.09), residues: 2912 sheet: -0.86 (0.74), residues: 48 loop : 0.15 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP j 48 HIS 0.014 0.002 HIS Z 21 PHE 0.024 0.002 PHE 3 23 TYR 0.022 0.002 TYR w 41 ARG 0.006 0.001 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 919 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8512 (m) cc_final: 0.7974 (t) REVERT: M 23 ASP cc_start: 0.7200 (t0) cc_final: 0.6695 (t0) REVERT: M 60 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7864 (mp) REVERT: M 122 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8309 (ttt) REVERT: H 184 LYS cc_start: 0.6929 (mmtp) cc_final: 0.6430 (ttmm) REVERT: D 5 TYR cc_start: 0.8708 (p90) cc_final: 0.8467 (p90) REVERT: E 18 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: F 15 ARG cc_start: 0.6922 (mmt90) cc_final: 0.6477 (mtp-110) REVERT: I 3 LYS cc_start: 0.8247 (mtpm) cc_final: 0.7888 (tppp) REVERT: I 5 TYR cc_start: 0.8415 (p90) cc_final: 0.8199 (p90) REVERT: K 5 TYR cc_start: 0.8098 (p90) cc_final: 0.7858 (p90) REVERT: K 9 MET cc_start: 0.7508 (tpp) cc_final: 0.7272 (mtm) REVERT: N 28 LEU cc_start: 0.9088 (tt) cc_final: 0.8872 (tp) REVERT: O 3 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7625 (tmtt) REVERT: Q 20 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: S 3 LYS cc_start: 0.8860 (mttt) cc_final: 0.8640 (mmtm) REVERT: S 14 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7743 (mtm180) REVERT: S 17 PHE cc_start: 0.8222 (m-80) cc_final: 0.7988 (m-10) REVERT: U 15 ARG cc_start: 0.7800 (mmt90) cc_final: 0.7173 (mtm110) REVERT: C 9 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: C 25 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8224 (mmm) REVERT: 1 5 TYR cc_start: 0.6125 (p90) cc_final: 0.5278 (p90) REVERT: 1 26 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8567 (mp) REVERT: 9 45 GLU cc_start: 0.7465 (tt0) cc_final: 0.7264 (tt0) REVERT: X 17 THR cc_start: 0.6704 (m) cc_final: 0.6116 (t) REVERT: X 28 MET cc_start: 0.6532 (tmm) cc_final: 0.6286 (tmm) REVERT: X 53 ARG cc_start: 0.6582 (mtt-85) cc_final: 0.5697 (ptm160) REVERT: Y 6 GLU cc_start: 0.6991 (tp30) cc_final: 0.6546 (pm20) REVERT: m 21 THR cc_start: 0.8597 (m) cc_final: 0.8139 (t) REVERT: m 23 ASP cc_start: 0.7151 (t0) cc_final: 0.6590 (t0) REVERT: a 9 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7778 (mtm) REVERT: e 18 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: f 15 ARG cc_start: 0.6983 (mmt90) cc_final: 0.6507 (mtp-110) REVERT: i 3 LYS cc_start: 0.8433 (mtpm) cc_final: 0.8017 (tppp) REVERT: i 5 TYR cc_start: 0.8232 (p90) cc_final: 0.7884 (p90) REVERT: j 32 SER cc_start: 0.8906 (p) cc_final: 0.8691 (m) REVERT: k 3 LYS cc_start: 0.8030 (tmtp) cc_final: 0.7660 (tptm) REVERT: n 16 GLN cc_start: 0.7319 (mt0) cc_final: 0.7081 (mt0) REVERT: o 3 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7692 (mtpp) REVERT: p 13 THR cc_start: 0.7614 (m) cc_final: 0.7362 (p) REVERT: r 7 LEU cc_start: 0.5085 (OUTLIER) cc_final: 0.4873 (tp) REVERT: s 14 ARG cc_start: 0.8340 (mtm110) cc_final: 0.7771 (mtt90) REVERT: u 15 ARG cc_start: 0.7749 (mmt90) cc_final: 0.7451 (mtt90) REVERT: v 14 ASP cc_start: 0.7546 (t70) cc_final: 0.7079 (t0) REVERT: v 16 GLN cc_start: 0.8025 (mt0) cc_final: 0.7809 (mt0) REVERT: w 37 SER cc_start: 0.8758 (OUTLIER) cc_final: 0.8488 (p) REVERT: 5 5 TYR cc_start: 0.7759 (p90) cc_final: 0.7501 (p90) REVERT: b1 4 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.5801 (m-80) REVERT: b1 37 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8538 (p) REVERT: b8 15 GLU cc_start: 0.7687 (mp0) cc_final: 0.7476 (pm20) REVERT: b9 10 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8595 (mt) REVERT: x 28 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.6055 (tpt) REVERT: x 53 ARG cc_start: 0.6497 (mtt-85) cc_final: 0.5603 (ptm160) REVERT: y 36 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8122 (tm) outliers start: 152 outliers final: 63 residues processed: 984 average time/residue: 0.9861 time to fit residues: 1255.8551 Evaluate side-chains 956 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 877 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain C residue 9 TYR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 1 residue 20 GLN Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 8 residue 7 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 30 MET Chi-restraints excluded: chain 0 residue 14 ASP Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain a residue 9 MET Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain k residue 7 ILE Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain r residue 7 LEU Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b8 residue 40 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 141 optimal weight: 2.9990 chunk 379 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 247 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 421 optimal weight: 0.8980 chunk 350 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 221 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 77 GLN ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN N 16 GLN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN 7 20 GLN 0 16 GLN l 199 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 42 ASN t 16 GLN c 18 GLN b1 20 GLN x 58 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 46700 Z= 0.216 Angle : 0.645 11.061 64138 Z= 0.283 Chirality : 0.038 0.231 6216 Planarity : 0.003 0.043 7888 Dihedral : 15.954 179.949 8464 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.68 % Allowed : 20.75 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.12), residues: 4462 helix: 2.28 (0.09), residues: 2922 sheet: -0.73 (0.75), residues: 48 loop : 0.18 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o 8 HIS 0.012 0.001 HIS Z 21 PHE 0.030 0.001 PHE x 47 TYR 0.021 0.001 TYR w 41 ARG 0.010 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 963 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8547 (m) cc_final: 0.7937 (t) REVERT: M 23 ASP cc_start: 0.7150 (t0) cc_final: 0.6638 (t0) REVERT: M 122 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8224 (ttt) REVERT: M 233 ARG cc_start: 0.7477 (ttp-110) cc_final: 0.6463 (ttm110) REVERT: H 173 GLU cc_start: 0.7997 (mp0) cc_final: 0.7588 (mm-30) REVERT: H 184 LYS cc_start: 0.6829 (mmtp) cc_final: 0.6337 (ttmm) REVERT: H 226 THR cc_start: 0.8724 (p) cc_final: 0.8328 (t) REVERT: D 5 TYR cc_start: 0.8698 (p90) cc_final: 0.8452 (p90) REVERT: E 7 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6309 (mt) REVERT: E 18 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: F 15 ARG cc_start: 0.6921 (mmt90) cc_final: 0.6496 (mtp-110) REVERT: G 12 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7714 (mt) REVERT: I 3 LYS cc_start: 0.8198 (mtpm) cc_final: 0.7859 (tppp) REVERT: K 3 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7677 (tptm) REVERT: O 3 LYS cc_start: 0.7995 (ttmm) cc_final: 0.7636 (tmtt) REVERT: S 3 LYS cc_start: 0.8880 (mttt) cc_final: 0.8661 (mmtm) REVERT: S 17 PHE cc_start: 0.8316 (m-80) cc_final: 0.8094 (m-10) REVERT: U 15 ARG cc_start: 0.7772 (mmt90) cc_final: 0.7152 (mtm110) REVERT: C 25 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: 2 15 GLU cc_start: 0.6592 (pm20) cc_final: 0.6031 (pm20) REVERT: 9 10 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8631 (mt) REVERT: 0 19 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8115 (pp20) REVERT: X 17 THR cc_start: 0.6851 (m) cc_final: 0.6245 (t) REVERT: X 28 MET cc_start: 0.6528 (tmm) cc_final: 0.6312 (tmm) REVERT: X 53 ARG cc_start: 0.6465 (mtt-85) cc_final: 0.5575 (ptm160) REVERT: Y 6 GLU cc_start: 0.6941 (tp30) cc_final: 0.6658 (tp30) REVERT: m 21 THR cc_start: 0.8494 (m) cc_final: 0.7996 (t) REVERT: m 23 ASP cc_start: 0.7117 (t0) cc_final: 0.6734 (t0) REVERT: h 173 GLU cc_start: 0.8013 (mp0) cc_final: 0.7658 (mm-30) REVERT: a 9 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7776 (mtm) REVERT: d 5 TYR cc_start: 0.8637 (p90) cc_final: 0.8354 (p90) REVERT: e 18 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7904 (mt0) REVERT: f 15 ARG cc_start: 0.6888 (mmt90) cc_final: 0.6422 (mtp-110) REVERT: i 3 LYS cc_start: 0.8411 (mtpm) cc_final: 0.8064 (tppp) REVERT: i 5 TYR cc_start: 0.8233 (p90) cc_final: 0.7893 (p90) REVERT: j 32 SER cc_start: 0.8891 (p) cc_final: 0.8677 (m) REVERT: k 3 LYS cc_start: 0.8092 (tmtp) cc_final: 0.7502 (tptm) REVERT: n 28 LEU cc_start: 0.9034 (tt) cc_final: 0.8771 (tp) REVERT: o 3 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7455 (tptm) REVERT: p 13 THR cc_start: 0.7533 (m) cc_final: 0.7326 (p) REVERT: r 7 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4814 (tp) REVERT: s 14 ARG cc_start: 0.8262 (mtm110) cc_final: 0.7792 (mtt90) REVERT: t 16 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7638 (mp10) REVERT: u 15 ARG cc_start: 0.7735 (mmt90) cc_final: 0.7454 (mtt90) REVERT: w 37 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8492 (p) REVERT: c 9 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.6810 (m-80) REVERT: 5 5 TYR cc_start: 0.7726 (p90) cc_final: 0.7515 (p90) REVERT: b1 4 PHE cc_start: 0.6295 (OUTLIER) cc_final: 0.5848 (m-10) REVERT: b1 37 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8515 (p) REVERT: 4 15 GLU cc_start: 0.7026 (pm20) cc_final: 0.6773 (pt0) REVERT: b9 10 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8593 (mt) REVERT: x 28 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6096 (tpt) REVERT: x 53 ARG cc_start: 0.6425 (mtt-85) cc_final: 0.5588 (ptm160) REVERT: y 6 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6213 (tp30) REVERT: y 36 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8129 (tm) outliers start: 140 outliers final: 56 residues processed: 1029 average time/residue: 0.9855 time to fit residues: 1332.8929 Evaluate side-chains 977 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 902 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 8 residue 7 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 0 residue 14 ASP Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain a residue 9 MET Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain k residue 6 LYS Chi-restraints excluded: chain k residue 7 ILE Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain r residue 7 LEU Chi-restraints excluded: chain t residue 16 GLN Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain y residue 6 GLU Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 406 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 308 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 355 optimal weight: 0.3980 chunk 235 optimal weight: 1.9990 chunk 420 optimal weight: 0.9990 chunk 262 optimal weight: 0.0170 chunk 256 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 16 GLN l 199 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 42 ASN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 16 GLN b1 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46700 Z= 0.193 Angle : 0.641 11.395 64138 Z= 0.282 Chirality : 0.038 0.227 6216 Planarity : 0.003 0.038 7888 Dihedral : 15.753 179.960 8464 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.28 % Allowed : 22.30 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.12), residues: 4462 helix: 2.38 (0.09), residues: 2910 sheet: -0.63 (0.75), residues: 48 loop : 0.19 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP j 29 HIS 0.011 0.001 HIS z 21 PHE 0.028 0.001 PHE K 17 TYR 0.027 0.001 TYR n 24 ARG 0.008 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 952 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8431 (m) cc_final: 0.7846 (t) REVERT: M 23 ASP cc_start: 0.7082 (t0) cc_final: 0.6529 (t0) REVERT: M 122 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8208 (ttt) REVERT: H 184 LYS cc_start: 0.6798 (mmtp) cc_final: 0.6308 (ttmm) REVERT: H 226 THR cc_start: 0.8704 (p) cc_final: 0.8295 (t) REVERT: A 22 VAL cc_start: 0.9208 (t) cc_final: 0.9003 (t) REVERT: D 5 TYR cc_start: 0.8680 (p90) cc_final: 0.8477 (p90) REVERT: E 26 SER cc_start: 0.8818 (m) cc_final: 0.8576 (p) REVERT: F 15 ARG cc_start: 0.6911 (mmt90) cc_final: 0.6500 (mtp-110) REVERT: I 3 LYS cc_start: 0.8187 (mtpm) cc_final: 0.7859 (tppp) REVERT: O 1 MET cc_start: 0.4387 (tmt) cc_final: 0.4116 (tmm) REVERT: O 3 LYS cc_start: 0.7919 (ttmm) cc_final: 0.7570 (tmtt) REVERT: S 3 LYS cc_start: 0.8889 (mttt) cc_final: 0.8622 (mmtm) REVERT: S 17 PHE cc_start: 0.8304 (m-80) cc_final: 0.8086 (m-10) REVERT: U 15 ARG cc_start: 0.7752 (mmt90) cc_final: 0.7141 (mtm110) REVERT: W 6 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8627 (mtmm) REVERT: C 25 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8211 (mmm) REVERT: 2 15 GLU cc_start: 0.6548 (pm20) cc_final: 0.6074 (pm20) REVERT: 9 10 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8597 (mt) REVERT: X 17 THR cc_start: 0.6784 (m) cc_final: 0.6198 (t) REVERT: X 28 MET cc_start: 0.6556 (tmm) cc_final: 0.6272 (tmm) REVERT: X 53 ARG cc_start: 0.6491 (mtt-85) cc_final: 0.5343 (ptm160) REVERT: Y 6 GLU cc_start: 0.6999 (tp30) cc_final: 0.6681 (tp30) REVERT: m 21 THR cc_start: 0.8420 (m) cc_final: 0.7951 (t) REVERT: m 23 ASP cc_start: 0.7143 (t0) cc_final: 0.6855 (t0) REVERT: h 195 MET cc_start: 0.7745 (mmm) cc_final: 0.7401 (mmm) REVERT: a 9 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8070 (mtt) REVERT: a 22 VAL cc_start: 0.9206 (t) cc_final: 0.9000 (t) REVERT: d 5 TYR cc_start: 0.8631 (p90) cc_final: 0.8390 (p90) REVERT: e 26 SER cc_start: 0.8774 (m) cc_final: 0.8549 (p) REVERT: f 15 ARG cc_start: 0.6882 (mmt90) cc_final: 0.6431 (mtp-110) REVERT: i 3 LYS cc_start: 0.8408 (mtpm) cc_final: 0.8015 (tppp) REVERT: i 5 TYR cc_start: 0.8222 (p90) cc_final: 0.7907 (p90) REVERT: k 3 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7360 (tptm) REVERT: k 6 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7504 (tptp) REVERT: o 3 LYS cc_start: 0.7996 (ttmm) cc_final: 0.7417 (tptm) REVERT: p 13 THR cc_start: 0.7490 (m) cc_final: 0.7281 (p) REVERT: q 6 LYS cc_start: 0.8299 (tppp) cc_final: 0.7914 (mmmt) REVERT: r 7 LEU cc_start: 0.4827 (OUTLIER) cc_final: 0.4616 (tp) REVERT: t 20 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8610 (tp) REVERT: u 15 ARG cc_start: 0.7730 (mmt90) cc_final: 0.7445 (mtt90) REVERT: c 9 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: 5 5 TYR cc_start: 0.7700 (p90) cc_final: 0.7488 (p90) REVERT: b1 37 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8526 (p) REVERT: 4 15 GLU cc_start: 0.7006 (pm20) cc_final: 0.6760 (pt0) REVERT: b9 10 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8593 (mt) REVERT: x 28 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6156 (tpt) REVERT: x 53 ARG cc_start: 0.6423 (mtt-85) cc_final: 0.5552 (ptm160) REVERT: x 54 MET cc_start: 0.7156 (mtp) cc_final: 0.6888 (mtp) REVERT: y 6 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6201 (tp30) REVERT: y 36 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8117 (tm) outliers start: 125 outliers final: 53 residues processed: 1007 average time/residue: 0.8722 time to fit residues: 1145.9747 Evaluate side-chains 972 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 904 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 8 residue 7 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain a residue 9 MET Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain k residue 6 LYS Chi-restraints excluded: chain k residue 7 ILE Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain r residue 7 LEU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain t residue 20 LEU Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain b1 residue 5 TYR Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain b8 residue 14 ASP Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain y residue 6 GLU Chi-restraints excluded: chain y residue 36 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 259 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 126 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 286 optimal weight: 0.0980 chunk 207 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 330 optimal weight: 2.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 266 HIS ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN 7 20 GLN 0 16 GLN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 199 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 20 GLN b1 20 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 46700 Z= 0.255 Angle : 0.680 12.372 64138 Z= 0.300 Chirality : 0.040 0.209 6216 Planarity : 0.003 0.035 7888 Dihedral : 15.804 179.947 8464 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.26 % Allowed : 22.66 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.12), residues: 4462 helix: 2.28 (0.09), residues: 2914 sheet: -0.60 (0.76), residues: 48 loop : 0.16 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 2 29 HIS 0.013 0.001 HIS z 21 PHE 0.027 0.001 PHE x 47 TYR 0.030 0.002 TYR N 24 ARG 0.005 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 922 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.7880 (t) REVERT: M 23 ASP cc_start: 0.7130 (t0) cc_final: 0.6527 (t0) REVERT: M 60 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7888 (mp) REVERT: M 122 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8289 (ttt) REVERT: H 173 GLU cc_start: 0.7947 (mp0) cc_final: 0.7552 (mm-30) REVERT: H 184 LYS cc_start: 0.6821 (mmtp) cc_final: 0.6311 (ttmm) REVERT: H 226 THR cc_start: 0.8710 (p) cc_final: 0.8333 (t) REVERT: E 26 SER cc_start: 0.8836 (m) cc_final: 0.8594 (p) REVERT: F 15 ARG cc_start: 0.6940 (mmt90) cc_final: 0.6515 (mtp-110) REVERT: I 39 PRO cc_start: 0.8749 (Cg_exo) cc_final: 0.8533 (Cg_endo) REVERT: N 28 LEU cc_start: 0.9061 (tt) cc_final: 0.8822 (tp) REVERT: O 3 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7577 (tmtt) REVERT: S 3 LYS cc_start: 0.8911 (mttt) cc_final: 0.8647 (mmtm) REVERT: S 17 PHE cc_start: 0.8318 (m-80) cc_final: 0.8114 (m-10) REVERT: U 15 ARG cc_start: 0.7775 (mmt90) cc_final: 0.7121 (mtm110) REVERT: W 6 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8624 (mtmm) REVERT: C 25 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8163 (mmm) REVERT: 1 4 PHE cc_start: 0.6048 (OUTLIER) cc_final: 0.5471 (m-10) REVERT: 1 25 PHE cc_start: 0.8365 (t80) cc_final: 0.8014 (t80) REVERT: 2 15 GLU cc_start: 0.6515 (pm20) cc_final: 0.6221 (pm20) REVERT: 9 10 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8629 (mt) REVERT: X 17 THR cc_start: 0.6784 (m) cc_final: 0.6188 (t) REVERT: X 53 ARG cc_start: 0.6519 (mtt-85) cc_final: 0.5386 (ptm160) REVERT: X 55 LEU cc_start: 0.8596 (mt) cc_final: 0.8277 (mt) REVERT: Y 6 GLU cc_start: 0.6987 (tp30) cc_final: 0.6683 (tp30) REVERT: m 23 ASP cc_start: 0.7269 (t0) cc_final: 0.6667 (t0) REVERT: h 173 GLU cc_start: 0.7962 (mp0) cc_final: 0.7611 (mm-30) REVERT: d 5 TYR cc_start: 0.8647 (p90) cc_final: 0.8423 (p90) REVERT: e 26 SER cc_start: 0.8827 (m) cc_final: 0.8612 (p) REVERT: f 15 ARG cc_start: 0.6934 (mmt90) cc_final: 0.6498 (mtp-110) REVERT: i 3 LYS cc_start: 0.8426 (mtpm) cc_final: 0.8059 (tppp) REVERT: i 5 TYR cc_start: 0.8235 (p90) cc_final: 0.7939 (p90) REVERT: k 3 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7469 (tptm) REVERT: k 6 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7529 (tptp) REVERT: o 3 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7454 (tptm) REVERT: p 10 THR cc_start: 0.6079 (OUTLIER) cc_final: 0.5822 (p) REVERT: r 7 LEU cc_start: 0.4753 (OUTLIER) cc_final: 0.4546 (tp) REVERT: t 16 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: u 15 ARG cc_start: 0.7731 (mmt90) cc_final: 0.7457 (mtt90) REVERT: 5 5 TYR cc_start: 0.7796 (p90) cc_final: 0.7535 (p90) REVERT: b1 37 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8512 (p) REVERT: 4 15 GLU cc_start: 0.7007 (pm20) cc_final: 0.6764 (pt0) REVERT: b9 10 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8578 (mt) REVERT: x 28 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6134 (tpt) REVERT: x 53 ARG cc_start: 0.6474 (mtt-85) cc_final: 0.5611 (ptm160) REVERT: x 54 MET cc_start: 0.7179 (mtp) cc_final: 0.6882 (mtp) REVERT: y 6 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6051 (tp30) REVERT: y 36 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8136 (tm) outliers start: 124 outliers final: 61 residues processed: 974 average time/residue: 0.8516 time to fit residues: 1081.7894 Evaluate side-chains 970 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 892 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 8 residue 7 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 252 VAL Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain k residue 6 LYS Chi-restraints excluded: chain k residue 7 ILE Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain r residue 7 LEU Chi-restraints excluded: chain r residue 30 LEU Chi-restraints excluded: chain t residue 16 GLN Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain b8 residue 14 ASP Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain y residue 6 GLU Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 382 optimal weight: 4.9990 chunk 402 optimal weight: 5.9990 chunk 367 optimal weight: 1.9990 chunk 391 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 353 optimal weight: 3.9990 chunk 370 optimal weight: 0.9980 chunk 390 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 266 HIS ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN 7 20 GLN 0 16 GLN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 199 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 46700 Z= 0.342 Angle : 0.755 14.335 64138 Z= 0.330 Chirality : 0.042 0.284 6216 Planarity : 0.004 0.040 7888 Dihedral : 16.126 179.952 8464 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.84 % Allowed : 23.50 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.12), residues: 4462 helix: 2.09 (0.09), residues: 2904 sheet: -0.70 (0.75), residues: 48 loop : 0.11 (0.17), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 29 HIS 0.012 0.002 HIS z 21 PHE 0.043 0.002 PHE k 23 TYR 0.028 0.002 TYR n 24 ARG 0.006 0.001 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 916 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.7969 (t) REVERT: M 23 ASP cc_start: 0.7109 (t0) cc_final: 0.6625 (t0) REVERT: H 184 LYS cc_start: 0.6928 (mmtp) cc_final: 0.6446 (ttmm) REVERT: H 226 THR cc_start: 0.8740 (p) cc_final: 0.8359 (t) REVERT: F 10 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7949 (mt) REVERT: F 15 ARG cc_start: 0.7064 (mmt90) cc_final: 0.6543 (mtp-110) REVERT: I 3 LYS cc_start: 0.8140 (mtpm) cc_final: 0.7835 (tppp) REVERT: K 6 LYS cc_start: 0.7859 (mmtm) cc_final: 0.7256 (mmmt) REVERT: K 15 ARG cc_start: 0.6934 (mmt180) cc_final: 0.6322 (mtm110) REVERT: N 28 LEU cc_start: 0.9028 (tt) cc_final: 0.8797 (tp) REVERT: O 3 LYS cc_start: 0.8001 (ttmm) cc_final: 0.7677 (tmtt) REVERT: S 3 LYS cc_start: 0.8957 (mttt) cc_final: 0.8706 (mmtm) REVERT: U 15 ARG cc_start: 0.7806 (mmt90) cc_final: 0.7070 (mtm110) REVERT: W 6 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8649 (mtmm) REVERT: 3 9 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7808 (mpp) REVERT: 1 4 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5553 (m-10) REVERT: 9 10 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8672 (mt) REVERT: X 17 THR cc_start: 0.6973 (m) cc_final: 0.6348 (t) REVERT: X 28 MET cc_start: 0.6484 (tmm) cc_final: 0.5817 (tpt) REVERT: X 53 ARG cc_start: 0.6497 (mtt-85) cc_final: 0.5566 (ptm160) REVERT: X 55 LEU cc_start: 0.8676 (mt) cc_final: 0.8370 (mt) REVERT: Y 6 GLU cc_start: 0.7048 (tp30) cc_final: 0.6745 (tp30) REVERT: m 23 ASP cc_start: 0.7319 (t0) cc_final: 0.6740 (t0) REVERT: m 168 MET cc_start: 0.7828 (mmm) cc_final: 0.7287 (mtm) REVERT: d 5 TYR cc_start: 0.8664 (p90) cc_final: 0.8401 (p90) REVERT: e 26 SER cc_start: 0.8888 (m) cc_final: 0.8644 (p) REVERT: f 15 ARG cc_start: 0.6969 (mmt90) cc_final: 0.6493 (mtp-110) REVERT: i 3 LYS cc_start: 0.8479 (mtpm) cc_final: 0.8069 (tppp) REVERT: i 5 TYR cc_start: 0.8258 (p90) cc_final: 0.7883 (p90) REVERT: k 3 LYS cc_start: 0.8044 (tmtp) cc_final: 0.7682 (tptm) REVERT: k 15 ARG cc_start: 0.6964 (mmt180) cc_final: 0.6401 (mtm110) REVERT: o 3 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7492 (tptm) REVERT: q 53 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.5462 (mtt-85) REVERT: u 15 ARG cc_start: 0.7786 (mmt90) cc_final: 0.7461 (mtt90) REVERT: 5 5 TYR cc_start: 0.7760 (p90) cc_final: 0.7498 (p90) REVERT: b1 37 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8515 (p) REVERT: 4 15 GLU cc_start: 0.7057 (pm20) cc_final: 0.6804 (pt0) REVERT: b9 10 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8616 (mt) REVERT: x 28 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6137 (tpt) REVERT: x 53 ARG cc_start: 0.6483 (mtt-85) cc_final: 0.5612 (ptm160) outliers start: 108 outliers final: 59 residues processed: 972 average time/residue: 0.8626 time to fit residues: 1090.5594 Evaluate side-chains 959 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 890 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 1 residue 5 TYR Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 8 residue 7 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 0 residue 16 GLN Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 252 VAL Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain q residue 53 ARG Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 257 optimal weight: 0.9990 chunk 414 optimal weight: 0.7980 chunk 252 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 434 optimal weight: 2.9990 chunk 399 optimal weight: 6.9990 chunk 345 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 267 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN Q 20 GLN 0 16 GLN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 20 GLN b1 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 46700 Z= 0.231 Angle : 0.698 12.514 64138 Z= 0.311 Chirality : 0.040 0.319 6216 Planarity : 0.003 0.031 7888 Dihedral : 15.886 179.978 8464 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.18 % Allowed : 24.84 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.12), residues: 4462 helix: 2.16 (0.09), residues: 2918 sheet: -0.66 (0.76), residues: 48 loop : 0.11 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP j 29 HIS 0.012 0.001 HIS z 21 PHE 0.045 0.001 PHE K 23 TYR 0.048 0.002 TYR 1 5 ARG 0.005 0.000 ARG Q 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 926 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8477 (m) cc_final: 0.7888 (t) REVERT: M 23 ASP cc_start: 0.7053 (t0) cc_final: 0.6650 (t0) REVERT: M 122 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8264 (ttt) REVERT: M 168 MET cc_start: 0.7703 (mmm) cc_final: 0.7128 (mtm) REVERT: H 184 LYS cc_start: 0.7003 (mmtp) cc_final: 0.6483 (ttmm) REVERT: H 193 MET cc_start: 0.7450 (mmt) cc_final: 0.7182 (mmm) REVERT: H 226 THR cc_start: 0.8713 (p) cc_final: 0.8344 (t) REVERT: H 242 MET cc_start: 0.8694 (ttm) cc_final: 0.8485 (ttt) REVERT: E 26 SER cc_start: 0.8826 (m) cc_final: 0.8599 (p) REVERT: F 15 ARG cc_start: 0.6981 (mmt90) cc_final: 0.6515 (mtp-110) REVERT: I 3 LYS cc_start: 0.8093 (mtpm) cc_final: 0.7807 (tppp) REVERT: K 6 LYS cc_start: 0.7912 (mmtm) cc_final: 0.7398 (mmpt) REVERT: K 15 ARG cc_start: 0.7014 (mmt180) cc_final: 0.6453 (mtm110) REVERT: K 20 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8205 (pm20) REVERT: N 28 LEU cc_start: 0.9015 (tt) cc_final: 0.8779 (tp) REVERT: O 3 LYS cc_start: 0.7908 (ttmm) cc_final: 0.7600 (tmtt) REVERT: O 5 TYR cc_start: 0.7567 (p90) cc_final: 0.7260 (p90) REVERT: P 20 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8553 (tp) REVERT: S 3 LYS cc_start: 0.8960 (mttt) cc_final: 0.8717 (mmtm) REVERT: U 15 ARG cc_start: 0.7742 (mmt90) cc_final: 0.7031 (mtm110) REVERT: W 6 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8603 (mtmm) REVERT: C 25 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8159 (mmm) REVERT: 1 4 PHE cc_start: 0.6005 (OUTLIER) cc_final: 0.5466 (m-10) REVERT: 2 15 GLU cc_start: 0.6766 (pm20) cc_final: 0.6552 (pt0) REVERT: 2 43 TYR cc_start: 0.7615 (t80) cc_final: 0.7392 (t80) REVERT: 9 10 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8641 (mt) REVERT: X 17 THR cc_start: 0.6918 (m) cc_final: 0.6296 (t) REVERT: X 28 MET cc_start: 0.6610 (tmm) cc_final: 0.5905 (tpt) REVERT: X 53 ARG cc_start: 0.6507 (mtt-85) cc_final: 0.5370 (ptm160) REVERT: Y 6 GLU cc_start: 0.6984 (tp30) cc_final: 0.6694 (tp30) REVERT: m 23 ASP cc_start: 0.7168 (t0) cc_final: 0.6804 (t0) REVERT: h 193 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7274 (tpt) REVERT: a 22 VAL cc_start: 0.9213 (t) cc_final: 0.9009 (t) REVERT: d 5 TYR cc_start: 0.8635 (p90) cc_final: 0.8384 (p90) REVERT: f 15 ARG cc_start: 0.6844 (mmt90) cc_final: 0.6442 (mtp-110) REVERT: i 3 LYS cc_start: 0.8467 (mtpm) cc_final: 0.8069 (tppp) REVERT: i 5 TYR cc_start: 0.8272 (p90) cc_final: 0.7886 (p90) REVERT: k 3 LYS cc_start: 0.8039 (tmtp) cc_final: 0.7684 (tptm) REVERT: k 9 MET cc_start: 0.7503 (tpp) cc_final: 0.7283 (mtm) REVERT: o 3 LYS cc_start: 0.8017 (ttmm) cc_final: 0.7498 (tptm) REVERT: o 5 TYR cc_start: 0.8062 (p90) cc_final: 0.7137 (p90) REVERT: p 20 LEU cc_start: 0.8770 (mt) cc_final: 0.8434 (tp) REVERT: u 15 ARG cc_start: 0.7779 (mmt90) cc_final: 0.7470 (mtt90) REVERT: v 15 GLU cc_start: 0.7234 (pp20) cc_final: 0.6864 (tm-30) REVERT: 5 5 TYR cc_start: 0.7675 (p90) cc_final: 0.7410 (p90) REVERT: b9 10 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8598 (mt) REVERT: x 28 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6121 (tpt) REVERT: x 53 ARG cc_start: 0.6426 (mtt-85) cc_final: 0.5522 (ptm160) outliers start: 83 outliers final: 51 residues processed: 969 average time/residue: 0.8167 time to fit residues: 1030.8747 Evaluate side-chains 960 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 899 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 193 MET Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain t residue 40 LEU Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 274 optimal weight: 0.9980 chunk 368 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 318 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 346 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 355 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 266 HIS K 52 ASN Q 20 GLN ** 2 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 16 GLN X 26 GLN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 20 GLN ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 20 GLN b1 20 GLN 4 16 GLN x 58 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112469 restraints weight = 64607.144| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.91 r_work: 0.3151 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 46700 Z= 0.273 Angle : 0.725 13.186 64138 Z= 0.321 Chirality : 0.041 0.362 6216 Planarity : 0.004 0.033 7888 Dihedral : 15.885 179.970 8464 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.23 % Allowed : 25.03 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.12), residues: 4462 helix: 2.11 (0.09), residues: 2914 sheet: -0.66 (0.76), residues: 48 loop : 0.09 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP j 29 HIS 0.012 0.002 HIS z 21 PHE 0.045 0.002 PHE k 23 TYR 0.031 0.002 TYR n 24 ARG 0.006 0.001 ARG Y 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16616.38 seconds wall clock time: 288 minutes 38.90 seconds (17318.90 seconds total)