Starting phenix.real_space_refine on Thu Dec 26 17:03:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vor_32058/12_2024/7vor_32058.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vor_32058/12_2024/7vor_32058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vor_32058/12_2024/7vor_32058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vor_32058/12_2024/7vor_32058.map" model { file = "/net/cci-nas-00/data/ceres_data/7vor_32058/12_2024/7vor_32058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vor_32058/12_2024/7vor_32058.cif" } resolution = 2.74 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= 0.003 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 24 5.49 5 Mg 64 5.21 5 S 174 5.16 5 C 31612 2.51 5 N 6300 2.21 5 O 6804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44980 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: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1973 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} 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: 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: "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: 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: "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: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" 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: "3" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 437 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} 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: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 392 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "2" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "0" 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: "X" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 529 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "Y" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 361 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} 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: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1973 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} 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: 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: "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: 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: "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: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "c" 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: "5" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 437 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} 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: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 392 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "4" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "b0" 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: "x" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 529 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "y" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 361 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "L" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 354 Unusual residues: {'BCL': 2, 'BPH': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 67 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: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 360 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "A" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 222 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 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: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "E" 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: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 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: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 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: "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: 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: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 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: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "Z" 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: "1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "2" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "7" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 122 Unusual residues: {'BCL': 2} 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: "9" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 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: "X" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 354 Unusual residues: {'BCL': 2, 'BPH': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 67 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: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 360 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "h" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "a" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 222 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 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: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "e" 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: "f" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "g" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 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: "r" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 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: "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: 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: "v" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 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: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "z" 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: "b1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "6" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 122 Unusual residues: {'BCL': 2} 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: "b9" 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: "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 Chain: "x" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.23, per 1000 atoms: 0.58 Number of scatterers: 44980 At special positions: 0 Unit cell: (225.68, 142.48, 107.12, 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 174 16.00 P 24 15.00 Mg 64 11.99 O 6804 8.00 N 6300 7.00 C 31612 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: 13.50 Conformation dependent library (CDL) restraints added in 4.8 seconds 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8576 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 14 sheets defined 73.2% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'L' and resid 5 through 10 removed outlier: 3.921A pdb=" N LYS L 8 " --> pdb=" O PHE L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 57 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.571A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 Processing helix chain 'L' and resid 151 through 164 removed outlier: 3.981A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 169 removed outlier: 6.013A 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 251 Processing helix chain 'L' and resid 258 through 268 removed outlier: 3.537A pdb=" N TRP L 262 " --> pdb=" O GLN L 258 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 41 Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 140 removed outlier: 3.572A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 178 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 227 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 263 through 287 removed outlier: 3.753A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'H' and resid 12 through 36 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: 3.995A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 removed outlier: 3.840A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 259 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 Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'B' and resid 13 through 46 Processing helix chain 'D' and resid 1 through 5 removed outlier: 4.436A pdb=" N TYR D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 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 2 through 10 removed outlier: 4.425A pdb=" N TYR F 5 " --> pdb=" O SER F 2 " (cutoff:3.500A) 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 51 Processing helix chain 'J' and resid 13 through 46 Processing helix chain 'K' and resid 3 through 10 Processing helix chain 'K' and resid 12 through 38 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 10 Processing helix chain 'O' and resid 12 through 38 Processing helix chain 'O' and resid 42 through 51 Processing helix chain 'P' and resid 13 through 46 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 51 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 10 removed outlier: 3.562A pdb=" N LYS U 6 " --> pdb=" O LYS U 3 " (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 51 Processing helix chain 'C' and resid 13 through 46 Processing helix chain '3' and resid 4 through 10 removed outlier: 3.615A pdb=" N ILE 3 7 " --> pdb=" O PHE 3 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE 3 10 " --> pdb=" O ILE 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 38 removed outlier: 3.647A pdb=" N THR 3 38 " --> pdb=" O ILE 3 34 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 51 Processing helix chain 'Z' and resid 13 through 46 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 '8' and resid 13 through 46 Processing helix chain '9' and resid 3 through 10 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 9 through 13 Processing helix chain 'X' and resid 14 through 55 Processing helix chain 'Y' and resid 5 through 29 Processing helix chain 'Y' and resid 31 through 49 removed outlier: 4.250A pdb=" N GLY Y 35 " --> pdb=" O HIS Y 31 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR Y 49 " --> pdb=" O PHE Y 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 10 removed outlier: 3.920A pdb=" N LYS l 8 " --> pdb=" O PHE l 5 " (cutoff:3.500A) Processing helix chain 'l' and resid 31 through 57 Processing helix chain 'l' and resid 70 through 74 Processing helix chain 'l' and resid 79 through 82 Processing helix chain 'l' and resid 83 through 112 Processing helix chain 'l' and resid 115 through 133 removed outlier: 3.571A pdb=" N PHE l 123 " --> pdb=" O PHE l 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 133 through 140 Processing helix chain 'l' and resid 141 through 145 Processing helix chain 'l' and resid 151 through 164 removed outlier: 3.981A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 165 through 169 removed outlier: 6.012A 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 251 Processing helix chain 'l' and resid 258 through 268 removed outlier: 3.537A pdb=" N TRP l 262 " --> pdb=" O GLN l 258 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP l 265 " --> pdb=" O ASP l 261 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP l 266 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 41 Processing helix chain 'm' and resid 53 through 78 Processing helix chain 'm' and resid 81 through 88 Processing helix chain 'm' and resid 98 through 102 Processing helix chain 'm' and resid 108 through 111 Processing helix chain 'm' and resid 112 through 140 removed outlier: 3.573A pdb=" N LEU m 140 " --> pdb=" O ARG m 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 144 through 162 Processing helix chain 'm' and resid 162 through 169 Processing helix chain 'm' and resid 170 through 174 Processing helix chain 'm' and resid 178 through 193 Processing helix chain 'm' and resid 195 through 198 Processing helix chain 'm' and resid 199 through 227 Processing helix chain 'm' and resid 228 through 230 No H-bonds generated for 'chain 'm' and resid 228 through 230' Processing helix chain 'm' and resid 233 through 240 Processing helix chain 'm' and resid 242 through 257 Processing helix chain 'm' and resid 263 through 287 removed outlier: 3.753A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 293 through 301 Processing helix chain 'h' and resid 12 through 36 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: 3.995A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) Processing helix chain 'h' and resid 226 through 244 removed outlier: 3.840A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 250 through 259 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 Processing helix chain 'a' and resid 12 through 38 Processing helix chain 'a' and resid 42 through 51 Processing helix chain 'b' and resid 13 through 46 Processing helix chain 'd' and resid 1 through 5 removed outlier: 4.436A pdb=" N TYR d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 11 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 2 through 10 removed outlier: 4.425A pdb=" N TYR f 5 " --> pdb=" O SER f 2 " (cutoff:3.500A) 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 51 Processing helix chain 'j' and resid 13 through 46 Processing helix chain 'k' and resid 3 through 10 Processing helix chain 'k' and resid 12 through 38 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 10 Processing helix chain 'o' and resid 12 through 38 Processing helix chain 'o' and resid 42 through 51 Processing helix chain 'p' and resid 13 through 46 Processing helix chain 'q' and resid 3 through 10 Processing helix chain 'q' and resid 12 through 38 Processing helix chain 'q' and resid 42 through 51 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 10 removed outlier: 3.562A pdb=" N LYS u 6 " --> pdb=" O LYS u 3 " (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 51 Processing helix chain 'c' and resid 13 through 46 Processing helix chain '5' and resid 4 through 10 removed outlier: 3.615A pdb=" N ILE 5 7 " --> pdb=" O PHE 5 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE 5 10 " --> pdb=" O ILE 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 38 removed outlier: 3.647A pdb=" N THR 5 38 " --> pdb=" O ILE 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 51 Processing helix chain 'z' and resid 13 through 46 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 'b8' and resid 13 through 46 Processing helix chain 'b9' and resid 3 through 10 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 9 through 13 Processing helix chain 'x' and resid 14 through 55 Processing helix chain 'y' and resid 5 through 29 Processing helix chain 'y' and resid 31 through 49 removed outlier: 4.250A pdb=" N GLY y 35 " --> pdb=" O HIS y 31 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR y 49 " --> pdb=" O PHE y 45 " (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 10 through 13 removed outlier: 6.551A 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: 3.662A 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: 5.665A pdb=" N VAL H 164 " --> pdb=" O GLU H 182 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU H 182 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP H 166 " --> pdb=" O GLU H 180 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP H 170 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 6.134A 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: 6.612A pdb=" N VAL H 153 " --> pdb=" O ALA H 161 " (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 10 through 13 removed outlier: 6.550A 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: 3.662A 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: 5.665A pdb=" N VAL h 164 " --> pdb=" O GLU h 182 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU h 182 " --> pdb=" O VAL h 164 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP h 166 " --> pdb=" O GLU h 180 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP h 170 " --> pdb=" O ALA h 176 " (cutoff:3.500A) removed outlier: 6.134A 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: 6.612A pdb=" N VAL h 153 " --> pdb=" O ALA h 161 " (cutoff:3.500A) 2646 hydrogen bonds defined for protein. 7458 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: 17.49 Time building geometry restraints manager: 14.86 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: 11995 1.35 - 1.55: 34061 1.55 - 1.76: 50 1.76 - 1.97: 338 1.97 - 2.18: 256 Bond restraints: 46700 Sorted by residual: bond pdb=" OB3 CDL M 407 " pdb=" PB2 CDL M 407 " ideal model delta sigma weight residual 1.529 1.455 0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" OB3 CDL m 407 " pdb=" PB2 CDL m 407 " ideal model delta sigma weight residual 1.529 1.456 0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" OA3 CDL m 407 " pdb=" PA1 CDL m 407 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" OA3 CDL M 407 " pdb=" PA1 CDL M 407 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" OB3 CDL F 102 " pdb=" PB2 CDL F 102 " ideal model delta sigma weight residual 1.529 1.459 0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 46695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 63687 4.66 - 9.31: 425 9.31 - 13.97: 28 13.97 - 18.62: 2 18.62 - 23.28: 14 Bond angle restraints: 64156 Sorted by residual: angle pdb=" O12 PC1 A 104 " pdb=" P PC1 A 104 " pdb=" O14 PC1 A 104 " ideal model delta sigma weight residual 123.67 100.39 23.28 3.00e+00 1.11e-01 6.02e+01 angle pdb=" O12 PC1 a 104 " pdb=" P PC1 a 104 " pdb=" O14 PC1 a 104 " ideal model delta sigma weight residual 123.67 100.41 23.26 3.00e+00 1.11e-01 6.01e+01 angle pdb=" O12 PC1 h 301 " pdb=" P PC1 h 301 " pdb=" O14 PC1 h 301 " ideal model delta sigma weight residual 123.67 100.85 22.82 3.00e+00 1.11e-01 5.78e+01 angle pdb=" O12 PC1 H 301 " pdb=" P PC1 H 301 " pdb=" O14 PC1 H 301 " ideal model delta sigma weight residual 123.67 100.85 22.82 3.00e+00 1.11e-01 5.78e+01 angle pdb=" O12 PC1 D 101 " pdb=" P PC1 D 101 " pdb=" O14 PC1 D 101 " ideal model delta sigma weight residual 123.67 100.96 22.71 3.00e+00 1.11e-01 5.73e+01 ... (remaining 64151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.57: 24094 31.57 - 63.13: 826 63.13 - 94.70: 94 94.70 - 126.27: 32 126.27 - 157.84: 2 Dihedral angle restraints: 25048 sinusoidal: 11706 harmonic: 13342 Sorted by residual: dihedral pdb=" C27 U10 l 304 " pdb=" C28 U10 l 304 " pdb=" C29 U10 l 304 " pdb=" C31 U10 l 304 " ideal model delta sinusoidal sigma weight residual -178.28 -20.45 -157.84 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C27 U10 L 304 " pdb=" C28 U10 L 304 " pdb=" C29 U10 L 304 " pdb=" C31 U10 L 304 " ideal model delta sinusoidal sigma weight residual -178.28 -20.48 -157.80 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C3M U10 L 305 " pdb=" C3 U10 L 305 " pdb=" O3 U10 L 305 " pdb=" C4 U10 L 305 " ideal model delta sinusoidal sigma weight residual 244.38 125.33 119.05 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 25045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4890 0.048 - 0.096: 1162 0.096 - 0.143: 176 0.143 - 0.191: 6 0.191 - 0.239: 8 Chirality restraints: 6242 Sorted by residual: chirality pdb=" C2C BPH m 404 " pdb=" C1C BPH m 404 " pdb=" C3C BPH m 404 " pdb=" CMC BPH m 404 " both_signs ideal model delta sigma weight residual False -2.81 -2.57 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2C BPH M 404 " pdb=" C1C BPH M 404 " pdb=" C3C BPH M 404 " pdb=" CMC BPH M 404 " both_signs ideal model delta sigma weight residual False -2.81 -2.57 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3C BPH L 303 " pdb=" C2C BPH L 303 " pdb=" C4C BPH L 303 " pdb=" CAC BPH L 303 " both_signs ideal model delta sigma weight residual False 2.83 2.61 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 6239 not shown) Planarity restraints: 7898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BPH m 404 " 0.013 2.00e-02 2.50e+03 4.75e-02 5.07e+01 pdb=" C1D BPH m 404 " 0.015 2.00e-02 2.50e+03 pdb=" C2D BPH m 404 " -0.024 2.00e-02 2.50e+03 pdb=" C3D BPH m 404 " -0.042 2.00e-02 2.50e+03 pdb=" C4D BPH m 404 " -0.024 2.00e-02 2.50e+03 pdb=" CAD BPH m 404 " 0.106 2.00e-02 2.50e+03 pdb=" CHA BPH m 404 " -0.045 2.00e-02 2.50e+03 pdb=" CHD BPH m 404 " 0.044 2.00e-02 2.50e+03 pdb=" CMD BPH m 404 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH M 404 " -0.013 2.00e-02 2.50e+03 4.74e-02 5.05e+01 pdb=" C1D BPH M 404 " -0.014 2.00e-02 2.50e+03 pdb=" C2D BPH M 404 " 0.024 2.00e-02 2.50e+03 pdb=" C3D BPH M 404 " 0.042 2.00e-02 2.50e+03 pdb=" C4D BPH M 404 " 0.023 2.00e-02 2.50e+03 pdb=" CAD BPH M 404 " -0.106 2.00e-02 2.50e+03 pdb=" CHA BPH M 404 " 0.045 2.00e-02 2.50e+03 pdb=" CHD BPH M 404 " -0.044 2.00e-02 2.50e+03 pdb=" CMD BPH M 404 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH l 303 " 0.016 2.00e-02 2.50e+03 3.05e-02 2.10e+01 pdb=" C1D BPH l 303 " 0.007 2.00e-02 2.50e+03 pdb=" C2D BPH l 303 " -0.017 2.00e-02 2.50e+03 pdb=" C3D BPH l 303 " -0.034 2.00e-02 2.50e+03 pdb=" C4D BPH l 303 " -0.015 2.00e-02 2.50e+03 pdb=" CAD BPH l 303 " 0.068 2.00e-02 2.50e+03 pdb=" CHA BPH l 303 " -0.027 2.00e-02 2.50e+03 pdb=" CHD BPH l 303 " 0.025 2.00e-02 2.50e+03 pdb=" CMD BPH l 303 " -0.021 2.00e-02 2.50e+03 ... (remaining 7895 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 856 2.69 - 3.24: 41146 3.24 - 3.80: 78267 3.80 - 4.35: 104984 4.35 - 4.90: 172799 Nonbonded interactions: 398052 Sorted by model distance: nonbonded pdb=" NE2 HIS l 190 " pdb="FE FE2 m 401 " model vdw 2.138 3.080 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE2 M 401 " model vdw 2.138 3.080 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE2 M 401 " model vdw 2.147 3.000 nonbonded pdb=" OE2 GLU m 234 " pdb="FE FE2 m 401 " model vdw 2.147 3.000 nonbonded pdb=" NE2 HIS m 219 " pdb="FE FE2 m 401 " model vdw 2.163 3.080 ... (remaining 398047 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 8 through 49) selection = (chain '8' and resid 8 through 49) selection = (chain 'B' and resid 8 through 49) selection = (chain 'C' and resid 8 through 49) selection = (chain 'E' and resid 8 through 49) selection = (chain 'G' and resid 8 through 49) selection = (chain 'J' and resid 8 through 49) selection = (chain 'N' and resid 8 through 49) selection = (chain 'P' and resid 8 through 49) selection = (chain 'R' and resid 8 through 49) selection = (chain 'T' and resid 8 through 49) selection = (chain 'V' and resid 8 through 49) selection = (chain 'Z' and resid 8 through 49) selection = (chain 'b' and resid 8 through 49) selection = (chain 'b0' and resid 8 through 49) selection = (chain 'b8' and resid 8 through 49) selection = (chain 'c' and resid 8 through 49) selection = (chain 'e' and resid 8 through 49) selection = (chain 'g' and resid 8 through 49) selection = (chain 'j' and resid 8 through 49) selection = (chain 'n' and resid 8 through 49) selection = (chain 'p' and resid 8 through 49) selection = (chain 'r' and resid 8 through 49) selection = (chain 't' and resid 8 through 49) selection = (chain 'v' and resid 8 through 49) selection = (chain 'z' and resid 8 through 49) } ncs_group { reference = (chain '1' and resid 8 through 48) selection = (chain '3' and resid 8 through 48) selection = (chain '5' and resid 8 through 48) selection = (chain '6' and resid 8 through 48) selection = (chain '7' and resid 8 through 48) selection = (chain 'I' and resid 8 through 48) selection = (chain 'K' and resid 8 through 48) selection = (chain 'O' and resid 8 through 48) selection = (chain 'U' and resid 8 through 48) selection = (chain 'W' and resid 8 through 48) selection = (chain 'b1' and resid 8 through 48) selection = (chain 'i' and resid 8 through 48) selection = (chain 'k' and resid 8 through 48) selection = (chain 'o' and resid 8 through 48) selection = (chain 'u' and resid 8 through 48) selection = (chain 'w' and resid 8 through 48) } ncs_group { reference = chain '2' selection = chain '4' } ncs_group { reference = (chain '9' and resid 1 through 55) selection = (chain 'A' and resid 1 through 55) selection = (chain 'D' and resid 1 through 55) selection = (chain 'F' and resid 1 through 55) selection = (chain 'Q' and resid 1 through 55) selection = (chain 'S' and resid 1 through 55) selection = (chain 'a' and resid 1 through 55) selection = (chain 'b9' and resid 1 through 55) selection = (chain 'd' and resid 1 through 55) selection = (chain 'f' and resid 1 through 55) selection = (chain 'q' and resid 1 through 55) selection = (chain 's' and resid 1 through 55) } 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: 3.950 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: 1.920 Check model and map are aligned: 0.360 Set scattering table: 0.440 Process input model: 95.000 Find NCS groups from input model: 3.960 Set up NCS constraints: 0.390 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:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.007 0.077 46700 Z= 0.415 Angle : 0.959 23.281 64156 Z= 0.376 Chirality : 0.040 0.239 6242 Planarity : 0.004 0.047 7898 Dihedral : 15.584 157.836 16472 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.37 % Allowed : 3.04 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.88 (0.12), residues: 4482 helix: 2.64 (0.09), residues: 2976 sheet: -0.81 (0.74), residues: 48 loop : 0.50 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP l 263 HIS 0.009 0.001 HIS l 153 PHE 0.018 0.001 PHE h 20 TYR 0.013 0.001 TYR m 198 ARG 0.004 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 871 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 168 MET cc_start: 0.8870 (mmm) cc_final: 0.8598 (mmm) REVERT: M 216 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8933 (t80) REVERT: H 134 MET cc_start: 0.7995 (ttp) cc_final: 0.7640 (ttp) REVERT: D 5 TYR cc_start: 0.9034 (p90) cc_final: 0.8715 (p90) REVERT: E 13 THR cc_start: 0.8286 (p) cc_final: 0.7939 (t) REVERT: F 15 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.7095 (mtm110) REVERT: G 25 MET cc_start: 0.8809 (mmm) cc_final: 0.8522 (mmt) REVERT: O 11 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: W 38 THR cc_start: 0.7978 (p) cc_final: 0.7613 (t) REVERT: C 25 MET cc_start: 0.7014 (mmm) cc_final: 0.6744 (tpp) REVERT: 8 25 MET cc_start: 0.8875 (mmm) cc_final: 0.8595 (mmm) REVERT: m 38 LEU cc_start: 0.9103 (tp) cc_final: 0.8896 (tp) REVERT: m 110 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7745 (mptt) REVERT: m 168 MET cc_start: 0.8878 (mmm) cc_final: 0.8529 (mmm) REVERT: h 134 MET cc_start: 0.7972 (ttp) cc_final: 0.7604 (ttp) REVERT: d 5 TYR cc_start: 0.9035 (p90) cc_final: 0.8726 (p90) REVERT: e 13 THR cc_start: 0.8299 (p) cc_final: 0.7948 (t) REVERT: f 15 ARG cc_start: 0.7521 (mtt-85) cc_final: 0.7121 (mtm110) REVERT: g 25 MET cc_start: 0.8811 (mmm) cc_final: 0.8528 (mmt) REVERT: n 14 ASP cc_start: 0.7638 (t70) cc_final: 0.7375 (t0) REVERT: o 11 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: c 25 MET cc_start: 0.6961 (mmm) cc_final: 0.6696 (tpp) REVERT: b8 25 MET cc_start: 0.8869 (mmm) cc_final: 0.8581 (mmm) outliers start: 14 outliers final: 1 residues processed: 883 average time/residue: 1.4073 time to fit residues: 1568.4248 Evaluate side-chains 694 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 690 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain o residue 11 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 0.6980 chunk 328 optimal weight: 0.7980 chunk 182 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 221 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 340 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 394 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN F 20 GLN J 16 GLN K 20 GLN N 16 GLN O 20 GLN Q 20 GLN ** V 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN 9 52 ASN X 10 HIS X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 77 GLN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN f 20 GLN j 16 GLN k 20 GLN n 16 GLN o 20 GLN q 20 GLN r 16 GLN ** v 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN b9 52 ASN x 10 HIS x 66 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 46700 Z= 0.235 Angle : 0.641 14.856 64156 Z= 0.270 Chirality : 0.038 0.163 6242 Planarity : 0.004 0.039 7898 Dihedral : 16.778 123.236 8438 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.70 % Allowed : 10.80 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.83 (0.12), residues: 4482 helix: 2.61 (0.09), residues: 2978 sheet: -0.70 (0.77), residues: 48 loop : 0.48 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 252 HIS 0.010 0.001 HIS M 266 PHE 0.019 0.001 PHE H 20 TYR 0.016 0.001 TYR O 5 ARG 0.005 0.001 ARG o 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 738 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 100 GLU cc_start: 0.7897 (pm20) cc_final: 0.7677 (pm20) REVERT: M 168 MET cc_start: 0.8802 (mmm) cc_final: 0.8495 (mmm) REVERT: M 236 GLU cc_start: 0.7556 (tp30) cc_final: 0.7354 (tp30) REVERT: H 134 MET cc_start: 0.7919 (ttp) cc_final: 0.7511 (ttp) REVERT: A 30 MET cc_start: 0.8206 (ttt) cc_final: 0.7971 (ttp) REVERT: D 5 TYR cc_start: 0.8891 (p90) cc_final: 0.8311 (p90) REVERT: D 38 THR cc_start: 0.8662 (p) cc_final: 0.8410 (p) REVERT: E 13 THR cc_start: 0.8237 (p) cc_final: 0.7711 (t) REVERT: E 14 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7456 (t70) REVERT: E 15 GLU cc_start: 0.7723 (mp0) cc_final: 0.7420 (mp0) REVERT: F 15 ARG cc_start: 0.7460 (mtt-85) cc_final: 0.7055 (mtm110) REVERT: G 25 MET cc_start: 0.8767 (mmm) cc_final: 0.8565 (mmp) REVERT: I 6 LYS cc_start: 0.9002 (mtpp) cc_final: 0.8770 (mtpp) REVERT: O 11 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: O 33 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8233 (tp) REVERT: W 30 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6360 (ptt) REVERT: C 25 MET cc_start: 0.7052 (mmm) cc_final: 0.6719 (tpp) REVERT: 8 25 MET cc_start: 0.8836 (mmm) cc_final: 0.8520 (mmm) REVERT: X 28 MET cc_start: 0.7561 (tpt) cc_final: 0.7234 (mmm) REVERT: X 61 GLN cc_start: 0.7517 (pt0) cc_final: 0.7290 (tt0) REVERT: l 20 ASN cc_start: 0.8827 (p0) cc_final: 0.8536 (p0) REVERT: l 155 ASP cc_start: 0.8674 (m-30) cc_final: 0.8367 (m-30) REVERT: m 100 GLU cc_start: 0.7900 (pm20) cc_final: 0.7622 (pm20) REVERT: m 110 LYS cc_start: 0.8004 (mtmm) cc_final: 0.7797 (mptt) REVERT: m 168 MET cc_start: 0.8814 (mmm) cc_final: 0.8596 (mmm) REVERT: m 216 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8912 (t80) REVERT: h 43 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: h 134 MET cc_start: 0.7899 (ttp) cc_final: 0.7509 (ttp) REVERT: a 30 MET cc_start: 0.8193 (ttt) cc_final: 0.7983 (ttt) REVERT: d 5 TYR cc_start: 0.8885 (p90) cc_final: 0.8308 (p90) REVERT: d 38 THR cc_start: 0.8662 (p) cc_final: 0.8413 (p) REVERT: e 13 THR cc_start: 0.8196 (p) cc_final: 0.7657 (t) REVERT: e 14 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7454 (t70) REVERT: e 15 GLU cc_start: 0.7730 (mp0) cc_final: 0.7429 (mp0) REVERT: f 15 ARG cc_start: 0.7467 (mtt-85) cc_final: 0.7030 (mtm110) REVERT: g 25 MET cc_start: 0.8767 (mmm) cc_final: 0.8482 (mmp) REVERT: i 6 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8746 (mtpp) REVERT: o 11 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: o 33 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8231 (tp) REVERT: c 25 MET cc_start: 0.7020 (mmm) cc_final: 0.6683 (tpp) REVERT: b8 25 MET cc_start: 0.8832 (mmm) cc_final: 0.8511 (mmm) REVERT: x 28 MET cc_start: 0.7574 (tpt) cc_final: 0.7290 (mmm) REVERT: x 61 GLN cc_start: 0.7498 (pt0) cc_final: 0.7252 (tt0) outliers start: 103 outliers final: 32 residues processed: 781 average time/residue: 1.3516 time to fit residues: 1333.9449 Evaluate side-chains 717 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 676 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain 3 residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 328 optimal weight: 0.7980 chunk 268 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 394 optimal weight: 0.6980 chunk 426 optimal weight: 0.2980 chunk 351 optimal weight: 9.9990 chunk 391 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 316 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN K 20 GLN O 20 GLN P 16 GLN Q 20 GLN T 16 GLN 8 18 GLN 9 52 ASN ** X 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 20 GLN n 16 GLN q 20 GLN r 16 GLN t 16 GLN b9 52 ASN ** x 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 46700 Z= 0.191 Angle : 0.608 14.572 64156 Z= 0.254 Chirality : 0.037 0.163 6242 Planarity : 0.003 0.037 7898 Dihedral : 16.196 121.956 8434 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.75 % Allowed : 10.80 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.77 (0.12), residues: 4482 helix: 2.59 (0.09), residues: 2990 sheet: -0.63 (0.77), residues: 48 loop : 0.34 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 252 HIS 0.009 0.001 HIS M 266 PHE 0.017 0.001 PHE H 20 TYR 0.019 0.001 TYR S 5 ARG 0.003 0.000 ARG o 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 702 time to evaluate : 4.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 139 MET cc_start: 0.9160 (mtp) cc_final: 0.8868 (mtm) REVERT: M 100 GLU cc_start: 0.7848 (pm20) cc_final: 0.7633 (pm20) REVERT: H 134 MET cc_start: 0.7880 (ttp) cc_final: 0.7492 (ttp) REVERT: A 30 MET cc_start: 0.8144 (ttt) cc_final: 0.7932 (ttp) REVERT: D 5 TYR cc_start: 0.8852 (p90) cc_final: 0.8307 (p90) REVERT: D 38 THR cc_start: 0.8627 (p) cc_final: 0.8423 (p) REVERT: E 13 THR cc_start: 0.8225 (p) cc_final: 0.7674 (t) REVERT: E 14 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7565 (t70) REVERT: E 15 GLU cc_start: 0.7684 (mp0) cc_final: 0.7454 (mp0) REVERT: F 6 LYS cc_start: 0.8695 (mttp) cc_final: 0.8465 (mttp) REVERT: F 9 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7924 (mpp) REVERT: F 15 ARG cc_start: 0.7483 (mtt-85) cc_final: 0.7128 (mtm110) REVERT: G 25 MET cc_start: 0.8760 (mmm) cc_final: 0.8552 (mmp) REVERT: I 6 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8524 (mtmm) REVERT: O 11 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: O 33 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8206 (tp) REVERT: W 15 ARG cc_start: 0.5554 (OUTLIER) cc_final: 0.4457 (mtp180) REVERT: C 25 MET cc_start: 0.7027 (mmm) cc_final: 0.6707 (tpp) REVERT: 3 9 MET cc_start: 0.3579 (mmm) cc_final: 0.2594 (mmm) REVERT: 8 25 MET cc_start: 0.8851 (mmm) cc_final: 0.8524 (mmm) REVERT: X 28 MET cc_start: 0.7638 (tpt) cc_final: 0.7314 (mmm) REVERT: l 155 ASP cc_start: 0.8675 (m-30) cc_final: 0.8358 (m-30) REVERT: m 100 GLU cc_start: 0.7852 (pm20) cc_final: 0.7639 (pm20) REVERT: m 168 MET cc_start: 0.8790 (mmm) cc_final: 0.8587 (mmm) REVERT: m 216 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8830 (t80) REVERT: h 43 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: h 134 MET cc_start: 0.7826 (ttp) cc_final: 0.7453 (ttp) REVERT: a 30 MET cc_start: 0.8141 (ttt) cc_final: 0.7929 (ttp) REVERT: d 3 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8147 (mttt) REVERT: d 5 TYR cc_start: 0.8846 (p90) cc_final: 0.8346 (p90) REVERT: e 13 THR cc_start: 0.8214 (p) cc_final: 0.7672 (t) REVERT: e 14 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7534 (t70) REVERT: e 15 GLU cc_start: 0.7687 (mp0) cc_final: 0.7456 (mp0) REVERT: f 9 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7947 (mpp) REVERT: f 15 ARG cc_start: 0.7468 (mtt-85) cc_final: 0.7125 (mtm110) REVERT: g 25 MET cc_start: 0.8759 (mmm) cc_final: 0.8549 (mmp) REVERT: i 6 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8516 (mtmm) REVERT: o 11 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: c 25 MET cc_start: 0.6988 (mmm) cc_final: 0.6656 (tpp) REVERT: 5 9 MET cc_start: 0.4344 (mmm) cc_final: 0.3319 (mmm) REVERT: b8 25 MET cc_start: 0.8849 (mmm) cc_final: 0.8519 (mmm) REVERT: x 28 MET cc_start: 0.7650 (tpt) cc_final: 0.7318 (mmm) outliers start: 105 outliers final: 39 residues processed: 743 average time/residue: 1.3011 time to fit residues: 1222.3612 Evaluate side-chains 720 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 670 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 15 ARG Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 242 MET Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 3 LYS Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain b9 residue 30 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 390 optimal weight: 7.9990 chunk 296 optimal weight: 0.1980 chunk 204 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 265 optimal weight: 0.6980 chunk 396 optimal weight: 0.0870 chunk 419 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 375 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 ASN H 68 HIS K 20 GLN R 16 GLN T 16 GLN 9 52 ASN X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 ASN h 68 HIS k 20 GLN r 16 GLN t 16 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 46700 Z= 0.172 Angle : 0.589 14.388 64156 Z= 0.246 Chirality : 0.037 0.164 6242 Planarity : 0.003 0.036 7898 Dihedral : 15.704 121.985 8434 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.04 % Allowed : 11.95 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.83 (0.12), residues: 4482 helix: 2.64 (0.09), residues: 2990 sheet: -0.54 (0.78), residues: 48 loop : 0.36 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 252 HIS 0.011 0.001 HIS l 190 PHE 0.016 0.001 PHE h 20 TYR 0.014 0.001 TYR j 24 ARG 0.002 0.000 ARG L 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 722 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 139 MET cc_start: 0.9121 (mtp) cc_final: 0.8882 (mtm) REVERT: L 155 ASP cc_start: 0.8602 (m-30) cc_final: 0.8298 (m-30) REVERT: M 216 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8902 (t80) REVERT: H 134 MET cc_start: 0.7808 (ttp) cc_final: 0.7424 (ttp) REVERT: A 30 MET cc_start: 0.8126 (ttt) cc_final: 0.7907 (ttt) REVERT: D 5 TYR cc_start: 0.8795 (p90) cc_final: 0.8258 (p90) REVERT: E 13 THR cc_start: 0.8203 (p) cc_final: 0.7911 (t) REVERT: E 14 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7542 (t70) REVERT: F 6 LYS cc_start: 0.8663 (mttp) cc_final: 0.8388 (mttp) REVERT: F 15 ARG cc_start: 0.7398 (mtt-85) cc_final: 0.7118 (mtm110) REVERT: I 6 LYS cc_start: 0.8786 (mtpp) cc_final: 0.8441 (mtmm) REVERT: I 51 TYR cc_start: 0.8836 (m-80) cc_final: 0.8600 (m-80) REVERT: O 11 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: W 15 ARG cc_start: 0.5508 (OUTLIER) cc_final: 0.4420 (mtp180) REVERT: C 25 MET cc_start: 0.6974 (mmm) cc_final: 0.6653 (tpp) REVERT: 1 30 MET cc_start: 0.5027 (tpt) cc_final: 0.4769 (tpt) REVERT: 8 25 MET cc_start: 0.8840 (mmm) cc_final: 0.8572 (mmm) REVERT: X 28 MET cc_start: 0.7653 (tpt) cc_final: 0.7323 (mmm) REVERT: X 61 GLN cc_start: 0.7566 (tt0) cc_final: 0.7263 (tt0) REVERT: l 23 ASP cc_start: 0.8976 (t70) cc_final: 0.8641 (t0) REVERT: l 72 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: l 155 ASP cc_start: 0.8679 (m-30) cc_final: 0.8361 (m-30) REVERT: m 168 MET cc_start: 0.8796 (mmm) cc_final: 0.8585 (mmm) REVERT: m 216 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8824 (t80) REVERT: h 43 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: h 134 MET cc_start: 0.7795 (ttp) cc_final: 0.7423 (ttp) REVERT: a 30 MET cc_start: 0.8118 (ttt) cc_final: 0.7905 (ttt) REVERT: d 5 TYR cc_start: 0.8822 (p90) cc_final: 0.8297 (p90) REVERT: e 13 THR cc_start: 0.8192 (p) cc_final: 0.7903 (t) REVERT: e 14 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7576 (t70) REVERT: f 5 TYR cc_start: 0.8943 (p90) cc_final: 0.8735 (p90) REVERT: f 6 LYS cc_start: 0.8679 (mttp) cc_final: 0.8465 (mttp) REVERT: f 9 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.7926 (mpp) REVERT: f 15 ARG cc_start: 0.7412 (mtt-85) cc_final: 0.7137 (mtm110) REVERT: i 6 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8440 (mtmm) REVERT: i 51 TYR cc_start: 0.8843 (m-80) cc_final: 0.8607 (m-80) REVERT: o 9 MET cc_start: 0.8252 (mmm) cc_final: 0.8030 (mmm) REVERT: o 11 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: c 25 MET cc_start: 0.6966 (mmm) cc_final: 0.6758 (tpp) REVERT: b1 30 MET cc_start: 0.5091 (tpt) cc_final: 0.4816 (tpt) REVERT: b8 25 MET cc_start: 0.8840 (mmm) cc_final: 0.8568 (mmm) REVERT: x 28 MET cc_start: 0.7672 (tpt) cc_final: 0.7345 (mmm) REVERT: x 61 GLN cc_start: 0.7610 (tt0) cc_final: 0.7326 (tt0) outliers start: 116 outliers final: 47 residues processed: 764 average time/residue: 1.2275 time to fit residues: 1187.1867 Evaluate side-chains 732 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 675 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 15 ARG Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain b9 residue 30 MET Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 357 optimal weight: 0.9990 chunk 289 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS B 16 GLN K 20 GLN O 20 GLN Q 20 GLN T 16 GLN 9 52 ASN X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 HIS b 16 GLN k 20 GLN n 16 GLN q 20 GLN t 16 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 46700 Z= 0.308 Angle : 0.678 14.165 64156 Z= 0.282 Chirality : 0.040 0.177 6242 Planarity : 0.004 0.038 7898 Dihedral : 15.990 121.080 8434 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.88 % Allowed : 12.84 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.54 (0.12), residues: 4482 helix: 2.39 (0.09), residues: 3006 sheet: -0.71 (0.76), residues: 48 loop : 0.29 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 252 HIS 0.009 0.002 HIS m 266 PHE 0.023 0.002 PHE l 216 TYR 0.015 0.002 TYR j 24 ARG 0.005 0.000 ARG M 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 704 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: L 139 MET cc_start: 0.9154 (mtp) cc_final: 0.8935 (mtm) REVERT: L 155 ASP cc_start: 0.8719 (m-30) cc_final: 0.8452 (m-30) REVERT: M 100 GLU cc_start: 0.7903 (pm20) cc_final: 0.7684 (pm20) REVERT: M 216 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8938 (t80) REVERT: H 134 MET cc_start: 0.7959 (ttp) cc_final: 0.7523 (ttp) REVERT: A 1 MET cc_start: 0.5595 (OUTLIER) cc_final: 0.3505 (mmt) REVERT: D 5 TYR cc_start: 0.8872 (p90) cc_final: 0.8305 (p90) REVERT: E 13 THR cc_start: 0.8345 (p) cc_final: 0.7849 (t) REVERT: E 14 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7577 (t70) REVERT: E 15 GLU cc_start: 0.7740 (mp0) cc_final: 0.7481 (mp0) REVERT: F 15 ARG cc_start: 0.7417 (mtt-85) cc_final: 0.7039 (mtm110) REVERT: I 6 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8468 (mtmm) REVERT: O 11 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: V 25 MET cc_start: 0.8277 (tpp) cc_final: 0.7547 (mmm) REVERT: W 15 ARG cc_start: 0.5600 (OUTLIER) cc_final: 0.4496 (mtp180) REVERT: 1 30 MET cc_start: 0.5001 (tpt) cc_final: 0.4709 (tpt) REVERT: X 61 GLN cc_start: 0.7798 (tt0) cc_final: 0.7543 (tt0) REVERT: l 72 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: l 155 ASP cc_start: 0.8686 (m-30) cc_final: 0.8400 (m-30) REVERT: m 168 MET cc_start: 0.8823 (mmm) cc_final: 0.8596 (mmm) REVERT: m 216 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8924 (t80) REVERT: h 43 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7104 (mm-30) REVERT: h 134 MET cc_start: 0.7942 (ttp) cc_final: 0.7511 (ttp) REVERT: a 1 MET cc_start: 0.5527 (OUTLIER) cc_final: 0.4065 (mmt) REVERT: d 5 TYR cc_start: 0.8872 (p90) cc_final: 0.8287 (p90) REVERT: e 13 THR cc_start: 0.8341 (p) cc_final: 0.7839 (t) REVERT: e 14 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7563 (t70) REVERT: e 15 GLU cc_start: 0.7767 (mp0) cc_final: 0.7510 (mp0) REVERT: f 15 ARG cc_start: 0.7451 (mtt-85) cc_final: 0.7066 (mtm110) REVERT: i 6 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8468 (mtmm) REVERT: i 51 TYR cc_start: 0.8860 (m-80) cc_final: 0.8629 (m-80) REVERT: o 9 MET cc_start: 0.8239 (mmm) cc_final: 0.7579 (mmt) REVERT: o 11 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: o 33 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8245 (tp) REVERT: v 25 MET cc_start: 0.8296 (tpp) cc_final: 0.7646 (mmm) REVERT: 5 9 MET cc_start: 0.4526 (mmm) cc_final: 0.3570 (mpp) REVERT: b1 30 MET cc_start: 0.4907 (tpt) cc_final: 0.4616 (tpt) REVERT: x 61 GLN cc_start: 0.7812 (tt0) cc_final: 0.7497 (tt0) outliers start: 110 outliers final: 54 residues processed: 737 average time/residue: 1.1346 time to fit residues: 1057.5028 Evaluate side-chains 743 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 676 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 15 ARG Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain 3 residue 45 GLU Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 105 MET Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain 5 residue 45 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 0.8980 chunk 377 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 419 optimal weight: 0.6980 chunk 348 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 ASN H 68 HIS B 16 GLN K 20 GLN O 20 GLN T 16 GLN 9 52 ASN X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 HIS b 16 GLN k 20 GLN o 20 GLN t 16 GLN b9 52 ASN x 18 ASN x 66 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 46700 Z= 0.217 Angle : 0.627 14.751 64156 Z= 0.261 Chirality : 0.038 0.156 6242 Planarity : 0.003 0.037 7898 Dihedral : 15.744 122.288 8434 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.73 % Allowed : 13.44 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.68 (0.12), residues: 4482 helix: 2.51 (0.09), residues: 2982 sheet: -0.62 (0.77), residues: 48 loop : 0.36 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP m 252 HIS 0.009 0.001 HIS L 190 PHE 0.019 0.001 PHE h 20 TYR 0.019 0.001 TYR J 24 ARG 0.002 0.000 ARG d 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 690 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 139 MET cc_start: 0.9168 (mtp) cc_final: 0.8939 (mtm) REVERT: L 155 ASP cc_start: 0.8684 (m-30) cc_final: 0.8395 (m-30) REVERT: M 100 GLU cc_start: 0.7872 (pm20) cc_final: 0.7652 (pm20) REVERT: M 216 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8935 (t80) REVERT: H 1 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7112 (tpp) REVERT: H 134 MET cc_start: 0.7902 (ttp) cc_final: 0.7469 (ttp) REVERT: A 1 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.3418 (mmt) REVERT: A 30 MET cc_start: 0.8194 (ttt) cc_final: 0.7981 (ttt) REVERT: D 5 TYR cc_start: 0.8833 (p90) cc_final: 0.8277 (p90) REVERT: E 13 THR cc_start: 0.8303 (p) cc_final: 0.7786 (t) REVERT: E 14 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7591 (t70) REVERT: E 15 GLU cc_start: 0.7772 (mp0) cc_final: 0.7533 (mp0) REVERT: F 9 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7910 (mpp) REVERT: F 15 ARG cc_start: 0.7391 (mtt-85) cc_final: 0.7083 (mtm110) REVERT: I 6 LYS cc_start: 0.8803 (mtpp) cc_final: 0.8500 (mtmm) REVERT: K 9 MET cc_start: 0.7789 (mtm) cc_final: 0.7545 (mmm) REVERT: O 11 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: V 25 MET cc_start: 0.8241 (tpp) cc_final: 0.7843 (mmm) REVERT: W 15 ARG cc_start: 0.5575 (OUTLIER) cc_final: 0.4470 (mtp180) REVERT: W 38 THR cc_start: 0.7796 (p) cc_final: 0.7464 (t) REVERT: 1 30 MET cc_start: 0.5040 (tpt) cc_final: 0.4780 (tpt) REVERT: X 61 GLN cc_start: 0.7790 (tt0) cc_final: 0.7553 (tt0) REVERT: l 72 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7653 (pt0) REVERT: l 155 ASP cc_start: 0.8697 (m-30) cc_final: 0.8410 (m-30) REVERT: m 168 MET cc_start: 0.8813 (mmm) cc_final: 0.8568 (mmm) REVERT: m 216 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8843 (t80) REVERT: h 43 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: h 134 MET cc_start: 0.7884 (ttp) cc_final: 0.7458 (ttp) REVERT: a 1 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.3436 (mmt) REVERT: a 3 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8294 (mtpt) REVERT: a 30 MET cc_start: 0.8192 (ttt) cc_final: 0.7977 (ttt) REVERT: d 5 TYR cc_start: 0.8824 (p90) cc_final: 0.8189 (p90) REVERT: e 13 THR cc_start: 0.8300 (p) cc_final: 0.7784 (t) REVERT: e 14 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7588 (t70) REVERT: e 15 GLU cc_start: 0.7765 (mp0) cc_final: 0.7526 (mp0) REVERT: f 15 ARG cc_start: 0.7387 (mtt-85) cc_final: 0.7071 (mtm110) REVERT: i 6 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8493 (mtmm) REVERT: o 9 MET cc_start: 0.8193 (mmm) cc_final: 0.7433 (mmt) REVERT: o 11 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: t 42 VAL cc_start: 0.9015 (t) cc_final: 0.8806 (t) REVERT: v 25 MET cc_start: 0.8229 (tpp) cc_final: 0.7820 (mmm) REVERT: w 38 THR cc_start: 0.7800 (p) cc_final: 0.7469 (t) REVERT: b1 30 MET cc_start: 0.4898 (tpt) cc_final: 0.4630 (tpt) REVERT: x 61 GLN cc_start: 0.7809 (tt0) cc_final: 0.7544 (tt0) outliers start: 104 outliers final: 49 residues processed: 734 average time/residue: 1.1543 time to fit residues: 1084.5567 Evaluate side-chains 732 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 670 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 15 ARG Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 404 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 353 optimal weight: 0.7980 chunk 234 optimal weight: 0.5980 chunk 418 optimal weight: 0.7980 chunk 261 optimal weight: 0.3980 chunk 255 optimal weight: 0.2980 chunk 193 optimal weight: 0.0370 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 ASN H 68 HIS K 20 GLN O 20 GLN T 16 GLN 8 18 GLN 9 52 ASN X 18 ASN X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 HIS k 20 GLN o 20 GLN t 16 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 46700 Z= 0.164 Angle : 0.597 14.600 64156 Z= 0.251 Chirality : 0.037 0.141 6242 Planarity : 0.003 0.036 7898 Dihedral : 15.372 122.533 8434 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.10 % Allowed : 14.39 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.80 (0.12), residues: 4482 helix: 2.61 (0.09), residues: 2990 sheet: -0.46 (0.78), residues: 48 loop : 0.37 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 252 HIS 0.013 0.001 HIS L 190 PHE 0.016 0.001 PHE H 20 TYR 0.021 0.001 TYR j 24 ARG 0.004 0.000 ARG n 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 710 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: L 155 ASP cc_start: 0.8596 (m-30) cc_final: 0.8289 (m-30) REVERT: L 205 GLU cc_start: 0.7720 (pt0) cc_final: 0.7408 (pm20) REVERT: M 100 GLU cc_start: 0.7827 (pm20) cc_final: 0.7615 (pm20) REVERT: H 1 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.7108 (tpp) REVERT: H 134 MET cc_start: 0.7812 (ttp) cc_final: 0.7425 (ttp) REVERT: A 30 MET cc_start: 0.8150 (ttt) cc_final: 0.7936 (ttp) REVERT: D 5 TYR cc_start: 0.8767 (p90) cc_final: 0.8187 (p90) REVERT: E 13 THR cc_start: 0.8304 (p) cc_final: 0.7830 (t) REVERT: E 14 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7642 (t70) REVERT: E 15 GLU cc_start: 0.7768 (mp0) cc_final: 0.7561 (mp0) REVERT: F 15 ARG cc_start: 0.7327 (mtt-85) cc_final: 0.7034 (mtm110) REVERT: I 6 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8452 (mtmm) REVERT: O 11 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: V 25 MET cc_start: 0.8202 (tpp) cc_final: 0.7659 (mmm) REVERT: W 15 ARG cc_start: 0.5536 (OUTLIER) cc_final: 0.4432 (mtp180) REVERT: C 25 MET cc_start: 0.6640 (tpp) cc_final: 0.6427 (tpp) REVERT: 3 9 MET cc_start: 0.3987 (mmm) cc_final: 0.3164 (mpp) REVERT: 1 30 MET cc_start: 0.5201 (tpt) cc_final: 0.4944 (tpt) REVERT: X 61 GLN cc_start: 0.7731 (tt0) cc_final: 0.7513 (tt0) REVERT: l 23 ASP cc_start: 0.8960 (t70) cc_final: 0.8677 (t0) REVERT: l 155 ASP cc_start: 0.8613 (m-30) cc_final: 0.8307 (m-30) REVERT: l 258 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8711 (mm110) REVERT: m 168 MET cc_start: 0.8774 (mmm) cc_final: 0.8537 (mmm) REVERT: m 216 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8853 (t80) REVERT: h 43 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7002 (mm-30) REVERT: h 134 MET cc_start: 0.7794 (ttp) cc_final: 0.7413 (ttp) REVERT: a 1 MET cc_start: 0.5391 (OUTLIER) cc_final: 0.3258 (mmt) REVERT: a 3 LYS cc_start: 0.8480 (mtpt) cc_final: 0.8266 (mtpt) REVERT: a 30 MET cc_start: 0.8149 (ttt) cc_final: 0.7932 (ttp) REVERT: d 5 TYR cc_start: 0.8794 (p90) cc_final: 0.8261 (p90) REVERT: e 13 THR cc_start: 0.8293 (p) cc_final: 0.7835 (t) REVERT: e 14 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7642 (t70) REVERT: e 15 GLU cc_start: 0.7765 (mp0) cc_final: 0.7564 (mp0) REVERT: f 15 ARG cc_start: 0.7353 (mtt-85) cc_final: 0.7084 (mtm110) REVERT: i 6 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8456 (mtmm) REVERT: i 51 TYR cc_start: 0.8838 (m-80) cc_final: 0.8580 (m-80) REVERT: o 9 MET cc_start: 0.8114 (mmm) cc_final: 0.7412 (mmt) REVERT: o 11 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: p 13 THR cc_start: 0.7955 (p) cc_final: 0.7351 (m) REVERT: c 25 MET cc_start: 0.6643 (tpp) cc_final: 0.6422 (tpp) REVERT: 5 9 MET cc_start: 0.4476 (mmm) cc_final: 0.3547 (mpp) REVERT: b1 30 MET cc_start: 0.5015 (tpt) cc_final: 0.4771 (tpt) REVERT: x 28 MET cc_start: 0.7481 (mmm) cc_final: 0.7259 (mmm) REVERT: x 61 GLN cc_start: 0.7778 (tt0) cc_final: 0.7563 (tt0) outliers start: 80 outliers final: 33 residues processed: 740 average time/residue: 1.0599 time to fit residues: 995.2930 Evaluate side-chains 728 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 684 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 15 ARG Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 258 GLN Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 105 MET Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 258 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 82 optimal weight: 0.0050 chunk 81 optimal weight: 3.9990 chunk 265 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 328 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS O 20 GLN R 16 GLN R 18 GLN T 16 GLN 9 52 ASN X 66 ASN l 60 ASN h 68 HIS n 16 GLN o 20 GLN r 16 GLN r 18 GLN t 16 GLN z 21 HIS b9 52 ASN x 66 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 46700 Z= 0.196 Angle : 0.622 14.251 64156 Z= 0.260 Chirality : 0.037 0.162 6242 Planarity : 0.003 0.037 7898 Dihedral : 15.356 121.912 8434 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.28 % Allowed : 14.36 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.77 (0.12), residues: 4482 helix: 2.59 (0.09), residues: 2982 sheet: -0.37 (0.78), residues: 48 loop : 0.36 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 252 HIS 0.009 0.001 HIS L 190 PHE 0.018 0.001 PHE H 20 TYR 0.038 0.001 TYR q 5 ARG 0.003 0.000 ARG n 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 685 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: L 155 ASP cc_start: 0.8611 (m-30) cc_final: 0.8306 (m-30) REVERT: L 205 GLU cc_start: 0.7733 (pt0) cc_final: 0.7410 (pm20) REVERT: M 100 GLU cc_start: 0.7828 (pm20) cc_final: 0.7620 (pm20) REVERT: H 134 MET cc_start: 0.7839 (ttp) cc_final: 0.7456 (ttp) REVERT: A 30 MET cc_start: 0.8138 (ttt) cc_final: 0.7931 (ttt) REVERT: D 5 TYR cc_start: 0.8747 (p90) cc_final: 0.8202 (p90) REVERT: E 13 THR cc_start: 0.8284 (p) cc_final: 0.7834 (t) REVERT: E 14 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7653 (t70) REVERT: F 6 LYS cc_start: 0.8645 (mttp) cc_final: 0.8292 (mttm) REVERT: F 9 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.7919 (mpp) REVERT: F 15 ARG cc_start: 0.7327 (mtt-85) cc_final: 0.7035 (mtm110) REVERT: I 6 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8474 (mtmm) REVERT: O 11 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: W 15 ARG cc_start: 0.5417 (OUTLIER) cc_final: 0.4344 (mtp180) REVERT: W 38 THR cc_start: 0.7717 (p) cc_final: 0.7396 (t) REVERT: 3 9 MET cc_start: 0.4291 (mmm) cc_final: 0.3318 (mpp) REVERT: 1 30 MET cc_start: 0.5024 (tpt) cc_final: 0.4772 (tpt) REVERT: X 61 GLN cc_start: 0.7809 (tt0) cc_final: 0.7581 (tt0) REVERT: l 23 ASP cc_start: 0.8965 (t70) cc_final: 0.8680 (t0) REVERT: l 155 ASP cc_start: 0.8691 (m-30) cc_final: 0.8403 (m-30) REVERT: l 205 GLU cc_start: 0.7725 (pt0) cc_final: 0.7417 (pm20) REVERT: l 258 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8737 (mm110) REVERT: m 168 MET cc_start: 0.8790 (mmm) cc_final: 0.8534 (mmm) REVERT: m 216 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8845 (t80) REVERT: h 43 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: h 134 MET cc_start: 0.7821 (ttp) cc_final: 0.7444 (ttp) REVERT: a 1 MET cc_start: 0.5418 (OUTLIER) cc_final: 0.3291 (mmt) REVERT: a 30 MET cc_start: 0.8135 (ttt) cc_final: 0.7927 (ttt) REVERT: d 5 TYR cc_start: 0.8792 (p90) cc_final: 0.8265 (p90) REVERT: e 13 THR cc_start: 0.8269 (p) cc_final: 0.7812 (t) REVERT: e 14 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7658 (t70) REVERT: f 15 ARG cc_start: 0.7332 (mtt-85) cc_final: 0.7022 (mtm110) REVERT: i 6 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8471 (mtmm) REVERT: o 9 MET cc_start: 0.8086 (mmm) cc_final: 0.7565 (mmt) REVERT: o 11 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: p 13 THR cc_start: 0.8009 (p) cc_final: 0.7447 (m) REVERT: v 25 MET cc_start: 0.8410 (mmm) cc_final: 0.7643 (mmm) REVERT: w 38 THR cc_start: 0.7728 (p) cc_final: 0.7410 (t) REVERT: 5 9 MET cc_start: 0.4624 (mmm) cc_final: 0.3600 (mpp) REVERT: b1 30 MET cc_start: 0.4915 (tpt) cc_final: 0.4680 (tpt) REVERT: x 61 GLN cc_start: 0.7795 (tt0) cc_final: 0.7558 (tt0) outliers start: 87 outliers final: 49 residues processed: 717 average time/residue: 1.0672 time to fit residues: 966.2864 Evaluate side-chains 733 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 673 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain U residue 11 PHE Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 15 ARG Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain 3 residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 258 GLN Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 105 MET Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 380 optimal weight: 4.9990 chunk 400 optimal weight: 0.7980 chunk 365 optimal weight: 0.8980 chunk 389 optimal weight: 7.9990 chunk 234 optimal weight: 0.5980 chunk 169 optimal weight: 0.1980 chunk 306 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 352 optimal weight: 1.9990 chunk 368 optimal weight: 3.9990 chunk 388 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS B 16 GLN O 20 GLN R 16 GLN R 18 GLN T 16 GLN Z 21 HIS 9 52 ASN X 66 ASN h 68 HIS n 16 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 16 GLN r 18 GLN t 16 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 46700 Z= 0.232 Angle : 0.646 14.297 64156 Z= 0.271 Chirality : 0.038 0.152 6242 Planarity : 0.003 0.037 7898 Dihedral : 15.426 121.881 8434 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.18 % Allowed : 14.86 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.69 (0.12), residues: 4482 helix: 2.53 (0.09), residues: 2982 sheet: -0.43 (0.77), residues: 48 loop : 0.32 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP m 252 HIS 0.009 0.001 HIS L 190 PHE 0.019 0.001 PHE h 20 TYR 0.019 0.001 TYR F 5 ARG 0.004 0.000 ARG l 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 683 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7627 (pt0) REVERT: L 139 MET cc_start: 0.9127 (mtp) cc_final: 0.8918 (mtm) REVERT: L 155 ASP cc_start: 0.8661 (m-30) cc_final: 0.8367 (m-30) REVERT: L 205 GLU cc_start: 0.7734 (pt0) cc_final: 0.7357 (pm20) REVERT: M 100 GLU cc_start: 0.7832 (pm20) cc_final: 0.7610 (pm20) REVERT: H 134 MET cc_start: 0.7887 (ttp) cc_final: 0.7502 (ttp) REVERT: A 30 MET cc_start: 0.8192 (ttt) cc_final: 0.7978 (ttt) REVERT: D 5 TYR cc_start: 0.8779 (p90) cc_final: 0.8219 (p90) REVERT: F 15 ARG cc_start: 0.7356 (mtt-85) cc_final: 0.7041 (mtm110) REVERT: I 6 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8478 (mtmm) REVERT: O 6 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7811 (mtmt) REVERT: O 11 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: O 33 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8282 (tp) REVERT: V 25 MET cc_start: 0.8392 (mmm) cc_final: 0.7563 (mmm) REVERT: W 15 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.4329 (mtp180) REVERT: W 38 THR cc_start: 0.7750 (p) cc_final: 0.7430 (t) REVERT: C 25 MET cc_start: 0.6759 (tpp) cc_final: 0.6521 (tpp) REVERT: 3 9 MET cc_start: 0.4406 (mmm) cc_final: 0.3373 (mpp) REVERT: 1 30 MET cc_start: 0.5049 (tpt) cc_final: 0.4774 (tpt) REVERT: X 61 GLN cc_start: 0.7832 (tt0) cc_final: 0.7598 (tt0) REVERT: l 23 ASP cc_start: 0.8998 (t70) cc_final: 0.8666 (t0) REVERT: l 155 ASP cc_start: 0.8696 (m-30) cc_final: 0.8403 (m-30) REVERT: l 205 GLU cc_start: 0.7779 (pt0) cc_final: 0.7448 (pm20) REVERT: l 258 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8774 (mm110) REVERT: m 168 MET cc_start: 0.8799 (mmm) cc_final: 0.8538 (mmm) REVERT: m 216 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8852 (t80) REVERT: h 43 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7044 (mm-30) REVERT: h 134 MET cc_start: 0.7868 (ttp) cc_final: 0.7465 (ttp) REVERT: a 1 MET cc_start: 0.5500 (OUTLIER) cc_final: 0.3380 (mmt) REVERT: a 30 MET cc_start: 0.8188 (ttt) cc_final: 0.7973 (ttt) REVERT: d 3 LYS cc_start: 0.8579 (mtpm) cc_final: 0.8278 (ttpt) REVERT: d 5 TYR cc_start: 0.8817 (p90) cc_final: 0.8233 (p90) REVERT: f 6 LYS cc_start: 0.8658 (mttp) cc_final: 0.8407 (mttm) REVERT: f 15 ARG cc_start: 0.7334 (mtt-85) cc_final: 0.7024 (mtm110) REVERT: i 6 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8479 (mtmm) REVERT: o 9 MET cc_start: 0.8031 (mmm) cc_final: 0.7562 (mmt) REVERT: o 11 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: o 33 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8291 (tp) REVERT: p 13 THR cc_start: 0.8032 (p) cc_final: 0.7479 (m) REVERT: v 25 MET cc_start: 0.8379 (mmm) cc_final: 0.7931 (mmm) REVERT: w 38 THR cc_start: 0.7804 (p) cc_final: 0.7480 (t) REVERT: c 25 MET cc_start: 0.6730 (tpp) cc_final: 0.6497 (tpp) REVERT: 5 9 MET cc_start: 0.4834 (mmm) cc_final: 0.3742 (mpp) REVERT: b1 30 MET cc_start: 0.4863 (tpt) cc_final: 0.4584 (tpt) REVERT: x 61 GLN cc_start: 0.7834 (tt0) cc_final: 0.7613 (tt0) outliers start: 83 outliers final: 49 residues processed: 725 average time/residue: 0.9932 time to fit residues: 909.5611 Evaluate side-chains 733 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 674 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 15 ARG Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 258 GLN Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 20 GLN Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 255 optimal weight: 0.9990 chunk 412 optimal weight: 0.8980 chunk 251 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 286 optimal weight: 0.8980 chunk 432 optimal weight: 1.9990 chunk 397 optimal weight: 8.9990 chunk 344 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 265 optimal weight: 0.5980 chunk 211 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS B 16 GLN O 20 GLN R 16 GLN T 16 GLN 9 52 ASN X 66 ASN h 68 HIS b 16 GLN n 16 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 16 GLN t 16 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 46700 Z= 0.225 Angle : 0.643 14.459 64156 Z= 0.271 Chirality : 0.038 0.148 6242 Planarity : 0.003 0.037 7898 Dihedral : 15.404 122.107 8434 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.78 % Allowed : 15.49 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.68 (0.12), residues: 4482 helix: 2.51 (0.09), residues: 2982 sheet: -0.45 (0.76), residues: 48 loop : 0.33 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 3 8 HIS 0.010 0.001 HIS L 190 PHE 0.025 0.001 PHE M 216 TYR 0.026 0.001 TYR O 5 ARG 0.004 0.000 ARG L 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 690 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: L 155 ASP cc_start: 0.8661 (m-30) cc_final: 0.8366 (m-30) REVERT: M 100 GLU cc_start: 0.7823 (pm20) cc_final: 0.7604 (pm20) REVERT: H 134 MET cc_start: 0.7886 (ttp) cc_final: 0.7477 (ttp) REVERT: A 30 MET cc_start: 0.8194 (ttt) cc_final: 0.7976 (ttt) REVERT: D 5 TYR cc_start: 0.8721 (p90) cc_final: 0.8311 (p90) REVERT: E 15 GLU cc_start: 0.7690 (mp0) cc_final: 0.7468 (mp0) REVERT: F 15 ARG cc_start: 0.7346 (mtt-85) cc_final: 0.7033 (mtm110) REVERT: I 6 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8476 (mtmm) REVERT: O 6 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7867 (mtmm) REVERT: O 11 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: O 33 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8278 (tp) REVERT: W 15 ARG cc_start: 0.5432 (OUTLIER) cc_final: 0.4340 (mtp180) REVERT: W 38 THR cc_start: 0.7755 (p) cc_final: 0.7438 (t) REVERT: C 25 MET cc_start: 0.6765 (tpp) cc_final: 0.6550 (tpp) REVERT: 1 30 MET cc_start: 0.4999 (tpt) cc_final: 0.4746 (tpt) REVERT: X 61 GLN cc_start: 0.7830 (tt0) cc_final: 0.7610 (tt0) REVERT: l 23 ASP cc_start: 0.8995 (t70) cc_final: 0.8663 (t0) REVERT: l 155 ASP cc_start: 0.8696 (m-30) cc_final: 0.8404 (m-30) REVERT: l 185 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.8861 (tp) REVERT: l 205 GLU cc_start: 0.7747 (pt0) cc_final: 0.7363 (pm20) REVERT: m 168 MET cc_start: 0.8798 (mmm) cc_final: 0.8537 (mmm) REVERT: m 216 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8851 (t80) REVERT: h 1 MET cc_start: 0.7264 (ttp) cc_final: 0.7050 (ttp) REVERT: h 43 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: h 134 MET cc_start: 0.7864 (ttp) cc_final: 0.7465 (ttp) REVERT: a 1 MET cc_start: 0.5500 (OUTLIER) cc_final: 0.3347 (mmt) REVERT: a 30 MET cc_start: 0.8191 (ttt) cc_final: 0.7975 (ttt) REVERT: d 3 LYS cc_start: 0.8583 (mtpm) cc_final: 0.8308 (ttpt) REVERT: d 5 TYR cc_start: 0.8761 (p90) cc_final: 0.8304 (p90) REVERT: f 15 ARG cc_start: 0.7331 (mtt-85) cc_final: 0.7027 (mtm110) REVERT: i 6 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8478 (mtmm) REVERT: o 9 MET cc_start: 0.8052 (mmm) cc_final: 0.7533 (mmt) REVERT: o 11 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: o 33 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8286 (tp) REVERT: p 13 THR cc_start: 0.8055 (p) cc_final: 0.7474 (m) REVERT: w 38 THR cc_start: 0.7799 (p) cc_final: 0.7480 (t) REVERT: c 25 MET cc_start: 0.6792 (tpp) cc_final: 0.6574 (tpp) REVERT: 5 9 MET cc_start: 0.4765 (mmm) cc_final: 0.3653 (mpp) REVERT: b1 30 MET cc_start: 0.4870 (tpt) cc_final: 0.4554 (tpt) REVERT: x 61 GLN cc_start: 0.7874 (tt0) cc_final: 0.7636 (tt0) outliers start: 68 outliers final: 53 residues processed: 723 average time/residue: 0.9963 time to fit residues: 908.2835 Evaluate side-chains 746 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 683 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 15 ARG Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 185 LEU Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 20 GLN Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 273 optimal weight: 0.8980 chunk 366 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 317 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 344 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 354 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS B 16 GLN O 20 GLN ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 16 GLN R 18 GLN T 16 GLN 9 52 ASN X 66 ASN h 68 HIS b 16 GLN n 16 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 16 GLN r 18 GLN t 16 GLN b9 52 ASN x 18 ASN x 66 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109828 restraints weight = 53986.714| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.33 r_work: 0.2858 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2033 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= 0.219 Angle : 0.643 14.493 64156 Z= 0.271 Chirality : 0.038 0.143 6242 Planarity : 0.003 0.036 7898 Dihedral : 15.367 122.251 8434 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.89 % Allowed : 15.62 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.67 (0.12), residues: 4482 helix: 2.49 (0.09), residues: 2994 sheet: -0.43 (0.77), residues: 48 loop : 0.34 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 3 8 HIS 0.010 0.001 HIS P 21 PHE 0.023 0.001 PHE M 216 TYR 0.018 0.001 TYR q 5 ARG 0.003 0.000 ARG M 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14904.95 seconds wall clock time: 260 minutes 15.34 seconds (15615.34 seconds total)