Starting phenix.real_space_refine on Wed Aug 27 03:14:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vot_32059/08_2025/7vot_32059.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vot_32059/08_2025/7vot_32059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vot_32059/08_2025/7vot_32059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vot_32059/08_2025/7vot_32059.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vot_32059/08_2025/7vot_32059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vot_32059/08_2025/7vot_32059.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 26 5.49 5 Mg 64 5.21 5 S 176 5.16 5 C 31648 2.51 5 N 6276 2.21 5 O 6792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44984 Number of models: 1 Model: "" Number of chains: 128 Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "H" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1955 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 234} Chain: "A" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "J" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "K" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "R" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "V" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "W" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "3" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "Z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "2" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 328 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "7" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "0" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "X" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "Y" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 375 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "l" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "h" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1955 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 234} Chain: "a" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "b" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "d" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "e" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "f" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "g" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "i" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "j" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "k" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "n" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "o" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "p" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "r" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "s" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "t" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "u" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "v" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "w" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "c" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "5" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "b1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "4" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 328 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "6" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "b8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "b9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "b0" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "x" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "y" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 375 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "L" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 412 Unusual residues: {'BCL': 3, 'BPB': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "M" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'BCL': 1, 'BPB': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'U10:plan-7': 1, 'U10:plan-8': 1} Unresolved non-hydrogen planarities: 32 Chain: "H" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 69 Chain: "A" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 220 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "9" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "l" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 412 Unusual residues: {'BCL': 3, 'BPB': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "m" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'BCL': 1, 'BPB': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'U10:plan-7': 1, 'U10:plan-8': 1} Unresolved non-hydrogen planarities: 32 Chain: "h" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 69 Chain: "a" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 220 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "b" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "e" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "j" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "o" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "s" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "v" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "w" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "b1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "b8" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "b9" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "b0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.75, per 1000 atoms: 0.24 Number of scatterers: 44984 At special positions: 0 Unit cell: (215.28, 140.4, 104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 176 16.00 P 26 15.00 Mg 64 11.99 O 6792 8.00 N 6276 7.00 C 31648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=64, symmetry=0 Number of additional bonds: simple=64, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.38 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8540 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 14 sheets defined 74.4% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 31 through 57 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.638A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU L 131 " --> pdb=" O ALA L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 Processing helix chain 'L' and resid 151 through 164 removed outlier: 3.734A pdb=" N ASP L 155 " --> pdb=" O TRP L 151 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 169 removed outlier: 5.947A pdb=" N HIS L 168 " --> pdb=" O GLY L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 Processing helix chain 'L' and resid 225 through 250 removed outlier: 3.627A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 263 removed outlier: 3.631A pdb=" N TRP L 262 " --> pdb=" O GLN L 258 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 258 through 263' Processing helix chain 'L' and resid 263 through 268 removed outlier: 3.902A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 43 removed outlier: 4.321A pdb=" N PHE M 42 " --> pdb=" O LEU M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 112 through 141 Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.663A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU M 156 " --> pdb=" O SER M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.509A pdb=" N GLU M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.622A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 removed outlier: 3.620A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 290 removed outlier: 3.605A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE M 282 " --> pdb=" O LEU M 278 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER M 287 " --> pdb=" O GLY M 283 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY M 288 " --> pdb=" O ILE M 284 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR M 289 " --> pdb=" O LEU M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 300 Processing helix chain 'H' and resid 12 through 35 Processing helix chain 'H' and resid 36 through 38 No H-bonds generated for 'chain 'H' and resid 36 through 38' Processing helix chain 'H' and resid 67 through 70 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.917A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 removed outlier: 3.978A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 248 Processing helix chain 'H' and resid 250 through 256 Processing helix chain 'A' and resid 3 through 5 No H-bonds generated for 'chain 'A' and resid 3 through 5' Processing helix chain 'A' and resid 6 through 11 removed outlier: 3.549A pdb=" N ILE A 10 " --> pdb=" O LYS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.598A pdb=" N THR A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.580A pdb=" N ALA A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 46 Processing helix chain 'D' and resid 1 through 5 removed outlier: 4.202A pdb=" N TYR D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 removed outlier: 3.501A pdb=" N ILE D 10 " --> pdb=" O LYS D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 38 Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'E' and resid 13 through 46 Processing helix chain 'F' and resid 1 through 5 removed outlier: 3.874A pdb=" N TYR F 5 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 11 Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'G' and resid 13 through 46 Processing helix chain 'I' and resid 3 through 5 No H-bonds generated for 'chain 'I' and resid 3 through 5' Processing helix chain 'I' and resid 6 through 11 removed outlier: 3.822A pdb=" N ILE I 10 " --> pdb=" O LYS I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 38 Processing helix chain 'I' and resid 42 through 52 Processing helix chain 'J' and resid 13 through 46 Processing helix chain 'K' and resid 3 through 5 No H-bonds generated for 'chain 'K' and resid 3 through 5' Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 12 through 38 Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'N' and resid 13 through 46 Processing helix chain 'O' and resid 3 through 5 No H-bonds generated for 'chain 'O' and resid 3 through 5' Processing helix chain 'O' and resid 6 through 11 Processing helix chain 'O' and resid 12 through 38 removed outlier: 3.608A pdb=" N THR O 38 " --> pdb=" O ILE O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 51 Processing helix chain 'P' and resid 13 through 46 Processing helix chain 'Q' and resid 1 through 10 removed outlier: 3.562A pdb=" N PHE Q 4 " --> pdb=" O MET Q 1 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR Q 5 " --> pdb=" O SER Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 51 removed outlier: 4.100A pdb=" N SER Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 46 Processing helix chain 'S' and resid 3 through 10 Processing helix chain 'S' and resid 12 through 38 Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 13 through 46 Processing helix chain 'U' and resid 3 through 5 No H-bonds generated for 'chain 'U' and resid 3 through 5' Processing helix chain 'U' and resid 6 through 11 removed outlier: 3.587A pdb=" N ILE U 10 " --> pdb=" O LYS U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 12 through 38 Processing helix chain 'U' and resid 42 through 51 Processing helix chain 'V' and resid 13 through 46 Processing helix chain 'W' and resid 3 through 10 Processing helix chain 'W' and resid 12 through 38 Processing helix chain 'W' and resid 42 through 52 Processing helix chain 'C' and resid 13 through 46 Processing helix chain '3' and resid 1 through 5 removed outlier: 3.979A pdb=" N PHE 3 4 " --> pdb=" O MET 3 1 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR 3 5 " --> pdb=" O SER 3 2 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 1 through 5' Processing helix chain '3' and resid 6 through 11 removed outlier: 3.965A pdb=" N ILE 3 10 " --> pdb=" O LYS 3 6 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 38 Processing helix chain '3' and resid 42 through 51 Processing helix chain 'Z' and resid 13 through 46 Processing helix chain '1' and resid 5 through 11 removed outlier: 3.752A pdb=" N MET 1 9 " --> pdb=" O TYR 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 38 Processing helix chain '1' and resid 42 through 51 Processing helix chain '2' and resid 13 through 46 Processing helix chain '7' and resid 3 through 10 Processing helix chain '7' and resid 12 through 38 Processing helix chain '7' and resid 42 through 47 removed outlier: 3.551A pdb=" N SER 7 47 " --> pdb=" O TRP 7 43 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 46 Processing helix chain '9' and resid 3 through 5 No H-bonds generated for 'chain '9' and resid 3 through 5' Processing helix chain '9' and resid 6 through 11 Processing helix chain '9' and resid 12 through 38 Processing helix chain '9' and resid 42 through 51 Processing helix chain '0' and resid 13 through 46 Processing helix chain 'X' and resid 18 through 55 Processing helix chain 'Y' and resid 5 through 29 Processing helix chain 'Y' and resid 31 through 48 removed outlier: 3.971A pdb=" N GLY Y 35 " --> pdb=" O HIS Y 31 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 10 Processing helix chain 'l' and resid 31 through 57 Processing helix chain 'l' and resid 70 through 74 Processing helix chain 'l' and resid 79 through 82 Processing helix chain 'l' and resid 83 through 112 Processing helix chain 'l' and resid 115 through 133 removed outlier: 3.638A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU l 131 " --> pdb=" O ALA l 127 " (cutoff:3.500A) Processing helix chain 'l' and resid 133 through 140 Processing helix chain 'l' and resid 141 through 145 Processing helix chain 'l' and resid 151 through 164 removed outlier: 3.735A pdb=" N ASP l 155 " --> pdb=" O TRP l 151 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 165 through 169 removed outlier: 5.947A pdb=" N HIS l 168 " --> pdb=" O GLY l 165 " (cutoff:3.500A) Processing helix chain 'l' and resid 170 through 199 Processing helix chain 'l' and resid 208 through 221 Processing helix chain 'l' and resid 225 through 250 removed outlier: 3.627A pdb=" N HIS l 230 " --> pdb=" O THR l 226 " (cutoff:3.500A) Processing helix chain 'l' and resid 258 through 263 removed outlier: 3.631A pdb=" N TRP l 262 " --> pdb=" O GLN l 258 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP l 263 " --> pdb=" O TRP l 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 258 through 263' Processing helix chain 'l' and resid 263 through 268 removed outlier: 3.903A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 43 removed outlier: 4.322A pdb=" N PHE m 42 " --> pdb=" O LEU m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 53 through 78 Processing helix chain 'm' and resid 81 through 88 Processing helix chain 'm' and resid 98 through 102 Processing helix chain 'm' and resid 112 through 141 Processing helix chain 'm' and resid 144 through 162 removed outlier: 3.662A pdb=" N ALA m 153 " --> pdb=" O ALA m 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU m 156 " --> pdb=" O SER m 152 " (cutoff:3.500A) Processing helix chain 'm' and resid 162 through 169 Processing helix chain 'm' and resid 170 through 174 removed outlier: 3.509A pdb=" N GLU m 173 " --> pdb=" O SER m 170 " (cutoff:3.500A) Processing helix chain 'm' and resid 178 through 193 removed outlier: 3.622A pdb=" N LEU m 183 " --> pdb=" O ILE m 179 " (cutoff:3.500A) Processing helix chain 'm' and resid 195 through 198 Processing helix chain 'm' and resid 199 through 226 Processing helix chain 'm' and resid 227 through 230 Processing helix chain 'm' and resid 233 through 240 Processing helix chain 'm' and resid 242 through 257 removed outlier: 3.620A pdb=" N TRP m 252 " --> pdb=" O ALA m 248 " (cutoff:3.500A) Processing helix chain 'm' and resid 263 through 290 removed outlier: 3.604A pdb=" N ARG m 267 " --> pdb=" O GLU m 263 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE m 282 " --> pdb=" O LEU m 278 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER m 287 " --> pdb=" O GLY m 283 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY m 288 " --> pdb=" O ILE m 284 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR m 289 " --> pdb=" O LEU m 285 " (cutoff:3.500A) Processing helix chain 'm' and resid 293 through 300 Processing helix chain 'h' and resid 12 through 35 Processing helix chain 'h' and resid 36 through 38 No H-bonds generated for 'chain 'h' and resid 36 through 38' Processing helix chain 'h' and resid 67 through 70 Processing helix chain 'h' and resid 103 through 108 Processing helix chain 'h' and resid 109 through 113 Processing helix chain 'h' and resid 194 through 196 No H-bonds generated for 'chain 'h' and resid 194 through 196' Processing helix chain 'h' and resid 209 through 216 removed outlier: 3.917A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) Processing helix chain 'h' and resid 226 through 244 removed outlier: 3.977A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 245 through 248 Processing helix chain 'h' and resid 250 through 256 Processing helix chain 'a' and resid 3 through 5 No H-bonds generated for 'chain 'a' and resid 3 through 5' Processing helix chain 'a' and resid 6 through 11 removed outlier: 3.549A pdb=" N ILE a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 38 removed outlier: 3.598A pdb=" N THR a 38 " --> pdb=" O ILE a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 51 removed outlier: 3.580A pdb=" N ALA a 48 " --> pdb=" O LEU a 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 46 Processing helix chain 'd' and resid 1 through 5 removed outlier: 4.202A pdb=" N TYR d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 11 removed outlier: 3.501A pdb=" N ILE d 10 " --> pdb=" O LYS d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 38 Processing helix chain 'd' and resid 42 through 51 Processing helix chain 'e' and resid 13 through 46 Processing helix chain 'f' and resid 1 through 5 removed outlier: 3.874A pdb=" N TYR f 5 " --> pdb=" O SER f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 11 Processing helix chain 'f' and resid 12 through 38 Processing helix chain 'f' and resid 42 through 51 Processing helix chain 'g' and resid 13 through 46 Processing helix chain 'i' and resid 3 through 10 Processing helix chain 'i' and resid 12 through 38 Processing helix chain 'i' and resid 42 through 52 Processing helix chain 'j' and resid 13 through 46 Processing helix chain 'k' and resid 3 through 5 No H-bonds generated for 'chain 'k' and resid 3 through 5' Processing helix chain 'k' and resid 6 through 11 Processing helix chain 'k' and resid 12 through 38 Processing helix chain 'k' and resid 42 through 51 Processing helix chain 'n' and resid 13 through 46 Processing helix chain 'o' and resid 3 through 5 No H-bonds generated for 'chain 'o' and resid 3 through 5' Processing helix chain 'o' and resid 6 through 11 Processing helix chain 'o' and resid 12 through 38 removed outlier: 3.609A pdb=" N THR o 38 " --> pdb=" O ILE o 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 51 Processing helix chain 'p' and resid 13 through 46 Processing helix chain 'q' and resid 1 through 10 removed outlier: 3.562A pdb=" N PHE q 4 " --> pdb=" O MET q 1 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR q 5 " --> pdb=" O SER q 2 " (cutoff:3.500A) Processing helix chain 'q' and resid 12 through 38 Processing helix chain 'q' and resid 42 through 51 removed outlier: 4.099A pdb=" N SER q 47 " --> pdb=" O TRP q 43 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA q 48 " --> pdb=" O LEU q 44 " (cutoff:3.500A) Processing helix chain 'r' and resid 13 through 46 Processing helix chain 's' and resid 3 through 10 Processing helix chain 's' and resid 12 through 38 Processing helix chain 's' and resid 42 through 51 Processing helix chain 't' and resid 13 through 46 Processing helix chain 'u' and resid 3 through 5 No H-bonds generated for 'chain 'u' and resid 3 through 5' Processing helix chain 'u' and resid 6 through 11 removed outlier: 3.587A pdb=" N ILE u 10 " --> pdb=" O LYS u 6 " (cutoff:3.500A) Processing helix chain 'u' and resid 12 through 38 Processing helix chain 'u' and resid 42 through 51 Processing helix chain 'v' and resid 13 through 46 Processing helix chain 'w' and resid 3 through 10 Processing helix chain 'w' and resid 12 through 38 Processing helix chain 'w' and resid 42 through 52 Processing helix chain 'c' and resid 13 through 46 Processing helix chain '5' and resid 1 through 5 removed outlier: 3.978A pdb=" N PHE 5 4 " --> pdb=" O MET 5 1 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR 5 5 " --> pdb=" O SER 5 2 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 1 through 5' Processing helix chain '5' and resid 6 through 11 removed outlier: 3.965A pdb=" N ILE 5 10 " --> pdb=" O LYS 5 6 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 38 Processing helix chain '5' and resid 42 through 51 Processing helix chain 'z' and resid 13 through 46 Processing helix chain 'b1' and resid 5 through 11 removed outlier: 3.753A pdb=" N METb1 9 " --> pdb=" O TYRb1 5 " (cutoff:3.500A) Processing helix chain 'b1' and resid 12 through 38 Processing helix chain 'b1' and resid 42 through 51 Processing helix chain '4' and resid 13 through 46 Processing helix chain '6' and resid 3 through 10 Processing helix chain '6' and resid 12 through 38 Processing helix chain '6' and resid 42 through 47 removed outlier: 3.551A pdb=" N SER 6 47 " --> pdb=" O TRP 6 43 " (cutoff:3.500A) Processing helix chain 'b8' and resid 13 through 46 Processing helix chain 'b9' and resid 3 through 5 No H-bonds generated for 'chain 'b9' and resid 3 through 5' Processing helix chain 'b9' and resid 6 through 11 Processing helix chain 'b9' and resid 12 through 38 Processing helix chain 'b9' and resid 42 through 51 Processing helix chain 'b0' and resid 13 through 46 Processing helix chain 'x' and resid 18 through 55 Processing helix chain 'y' and resid 5 through 29 Processing helix chain 'y' and resid 31 through 48 removed outlier: 3.970A pdb=" N GLY y 35 " --> pdb=" O HIS y 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.506A pdb=" N GLN M 11 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.604A pdb=" N PHE H 7 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 62 through 65 Processing sheet with id=AA5, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA6, first strand: chain 'H' and resid 131 through 133 removed outlier: 5.707A pdb=" N VAL H 164 " --> pdb=" O GLU H 182 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLU H 182 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP H 170 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA H 176 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.789A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'l' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'm' and resid 11 through 12 removed outlier: 6.506A pdb=" N GLN m 11 " --> pdb=" O SER h 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'h' and resid 5 through 7 removed outlier: 3.604A pdb=" N PHE h 7 " --> pdb=" O PHE h 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'h' and resid 62 through 65 Processing sheet with id=AB3, first strand: chain 'h' and resid 87 through 89 Processing sheet with id=AB4, first strand: chain 'h' and resid 131 through 133 removed outlier: 5.707A pdb=" N VAL h 164 " --> pdb=" O GLU h 182 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLU h 182 " --> pdb=" O VAL h 164 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ASP h 170 " --> pdb=" O ALA h 176 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA h 176 " --> pdb=" O ASP h 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 131 through 133 removed outlier: 3.788A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 2568 hydrogen bonds defined for protein. 7407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.89 Time building geometry restraints manager: 5.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 12008 1.35 - 1.56: 34042 1.56 - 1.76: 52 1.76 - 1.97: 342 1.97 - 2.17: 256 Bond restraints: 46700 Sorted by residual: bond pdb=" C3C BPB L 303 " pdb=" CAC BPB L 303 " ideal model delta sigma weight residual 1.334 1.551 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C3C BPB l 303 " pdb=" CAC BPB l 303 " ideal model delta sigma weight residual 1.334 1.551 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C3C BPB M 403 " pdb=" CAC BPB M 403 " ideal model delta sigma weight residual 1.334 1.546 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3C BPB m 403 " pdb=" CAC BPB m 403 " ideal model delta sigma weight residual 1.334 1.546 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" OB3 CDL m 406 " pdb=" PB2 CDL m 406 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.00e-02 1.00e+04 5.21e+01 ... (remaining 46695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 63326 3.25 - 6.49: 739 6.49 - 9.74: 49 9.74 - 12.99: 12 12.99 - 16.24: 12 Bond angle restraints: 64138 Sorted by residual: angle pdb=" C51 CDL m 406 " pdb=" CB5 CDL m 406 " pdb=" OB6 CDL m 406 " ideal model delta sigma weight residual 111.33 120.72 -9.39 1.32e+00 5.72e-01 5.05e+01 angle pdb=" C51 CDL M 406 " pdb=" CB5 CDL M 406 " pdb=" OB6 CDL M 406 " ideal model delta sigma weight residual 111.33 120.72 -9.39 1.32e+00 5.72e-01 5.04e+01 angle pdb=" C11 CDL h 303 " pdb=" CA5 CDL h 303 " pdb=" OA6 CDL h 303 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.51e+01 angle pdb=" C11 CDL H 303 " pdb=" CA5 CDL H 303 " pdb=" OA6 CDL H 303 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.51e+01 angle pdb=" C11 CDL m 406 " pdb=" CA5 CDL m 406 " pdb=" OA6 CDL m 406 " ideal model delta sigma weight residual 111.33 120.07 -8.74 1.32e+00 5.72e-01 4.37e+01 ... (remaining 64133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 24388 35.97 - 71.94: 550 71.94 - 107.92: 70 107.92 - 143.89: 10 143.89 - 179.86: 4 Dihedral angle restraints: 25022 sinusoidal: 11736 harmonic: 13286 Sorted by residual: dihedral pdb=" C1 BCL G 101 " pdb=" C2 BCL G 101 " pdb=" C3 BCL G 101 " pdb=" C5 BCL G 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.14 179.86 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL g 101 " pdb=" C2 BCL g 101 " pdb=" C3 BCL g 101 " pdb=" C5 BCL g 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.19 179.81 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 2 101 " pdb=" C2 BCL 2 101 " pdb=" C3 BCL 2 101 " pdb=" C5 BCL 2 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.54 -179.46 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 25019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4686 0.042 - 0.084: 1306 0.084 - 0.126: 203 0.126 - 0.168: 12 0.168 - 0.210: 9 Chirality restraints: 6216 Sorted by residual: chirality pdb=" C2C BPB m 403 " pdb=" C1C BPB m 403 " pdb=" C3C BPB m 403 " pdb=" CMC BPB m 403 " both_signs ideal model delta sigma weight residual False -2.78 -2.57 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C2C BPB M 403 " pdb=" C1C BPB M 403 " pdb=" C3C BPB M 403 " pdb=" CMC BPB M 403 " both_signs ideal model delta sigma weight residual False -2.78 -2.57 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG M 247 " pdb=" N ARG M 247 " pdb=" C ARG M 247 " pdb=" CB ARG M 247 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 6213 not shown) Planarity restraints: 7888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2C BPB L 303 " -0.381 2.00e-02 2.50e+03 5.00e-01 3.13e+03 pdb=" C3C BPB L 303 " 0.502 2.00e-02 2.50e+03 pdb=" C4C BPB L 303 " -0.207 2.00e-02 2.50e+03 pdb=" CAC BPB L 303 " 0.678 2.00e-02 2.50e+03 pdb=" CBC BPB L 303 " -0.591 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB l 303 " 0.382 2.00e-02 2.50e+03 5.00e-01 3.12e+03 pdb=" C3C BPB l 303 " -0.502 2.00e-02 2.50e+03 pdb=" C4C BPB l 303 " 0.207 2.00e-02 2.50e+03 pdb=" CAC BPB l 303 " -0.678 2.00e-02 2.50e+03 pdb=" CBC BPB l 303 " 0.591 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB M 403 " -0.007 2.00e-02 2.50e+03 2.37e-01 7.03e+02 pdb=" C3C BPB M 403 " -0.333 2.00e-02 2.50e+03 pdb=" C4C BPB M 403 " 0.140 2.00e-02 2.50e+03 pdb=" CAC BPB M 403 " 0.356 2.00e-02 2.50e+03 pdb=" CBC BPB M 403 " -0.156 2.00e-02 2.50e+03 ... (remaining 7885 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 959 2.70 - 3.25: 42141 3.25 - 3.80: 77296 3.80 - 4.35: 105442 4.35 - 4.90: 171473 Nonbonded interactions: 397311 Sorted by model distance: nonbonded pdb=" NE2 HIS l 190 " pdb="FE FE2 m 401 " model vdw 2.147 3.080 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE2 M 401 " model vdw 2.147 3.080 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE2 M 401 " model vdw 2.150 3.000 nonbonded pdb=" OE1 GLU m 234 " pdb="FE FE2 m 401 " model vdw 2.151 3.000 nonbonded pdb=" NE2 HIS M 219 " pdb="FE FE2 M 401 " model vdw 2.158 3.080 ... (remaining 397306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = (chain '0' and resid 10 through 49) selection = (chain '2' and resid 10 through 49) selection = (chain '4' and resid 10 through 49) selection = (chain '8' and resid 10 through 49) selection = (chain 'B' and resid 10 through 49) selection = (chain 'C' and resid 10 through 49) selection = (chain 'E' and resid 10 through 49) selection = (chain 'G' and resid 10 through 49) selection = (chain 'J' and resid 10 through 49) selection = (chain 'N' and resid 10 through 49) selection = (chain 'P' and resid 10 through 49) selection = (chain 'R' and resid 10 through 49) selection = (chain 'T' and resid 10 through 49) selection = (chain 'V' and resid 10 through 49) selection = (chain 'Z' and resid 10 through 49) selection = (chain 'b' and resid 10 through 49) selection = (chain 'b0' and resid 10 through 49) selection = (chain 'b8' and resid 10 through 49) selection = (chain 'c' and resid 10 through 49) selection = (chain 'e' and resid 10 through 49) selection = (chain 'g' and resid 10 through 49) selection = (chain 'j' and resid 10 through 49) selection = (chain 'n' and resid 10 through 49) selection = (chain 'p' and resid 10 through 49) selection = (chain 'r' and resid 10 through 49) selection = (chain 't' and resid 10 through 49) selection = (chain 'v' and resid 10 through 49) selection = (chain 'z' and resid 10 through 49) } ncs_group { reference = (chain '1' and resid 2 through 48) selection = (chain '3' and resid 2 through 48) selection = (chain '5' and resid 2 through 48) selection = (chain '6' and resid 2 through 48) selection = (chain '7' and resid 2 through 48) selection = (chain '9' and resid 2 through 48) selection = (chain 'A' and resid 2 through 48) selection = (chain 'D' and resid 2 through 48) selection = (chain 'F' and resid 2 through 48) selection = (chain 'I' and resid 2 through 48) selection = (chain 'K' and resid 2 through 48) selection = (chain 'O' and resid 2 through 48) selection = (chain 'Q' and resid 2 through 48) selection = (chain 'S' and resid 2 through 48) selection = (chain 'U' and resid 2 through 48) selection = (chain 'W' and resid 2 through 48) selection = (chain 'a' and resid 2 through 48) selection = (chain 'b1' and resid 2 through 48) selection = (chain 'b9' and resid 2 through 48) selection = (chain 'd' and resid 2 through 48) selection = (chain 'f' and resid 2 through 48) selection = (chain 'i' and resid 2 through 48) selection = (chain 'k' and resid 2 through 48) selection = (chain 'o' and resid 2 through 48) selection = (chain 'q' and resid 2 through 48) selection = (chain 's' and resid 2 through 48) selection = (chain 'u' and resid 2 through 48) selection = (chain 'w' and resid 2 through 48) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'Y' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.730 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: 0.060 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 39.920 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.217 46764 Z= 0.532 Angle : 0.796 16.237 64138 Z= 0.329 Chirality : 0.038 0.210 6216 Planarity : 0.009 0.500 7888 Dihedral : 15.277 179.859 16482 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.37 % Allowed : 3.31 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.12), residues: 4462 helix: 2.48 (0.09), residues: 2912 sheet: -0.44 (0.84), residues: 48 loop : 0.42 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.013 0.001 TYR a 41 PHE 0.016 0.001 PHE l 216 TRP 0.011 0.001 TRP L 263 HIS 0.009 0.001 HIS l 153 Details of bonding type rmsd covalent geometry : bond 0.00596 (46700) covalent geometry : angle 0.79647 (64138) hydrogen bonds : bond 0.19218 ( 2564) hydrogen bonds : angle 5.78209 ( 7407) Misc. bond : bond 0.11757 ( 64) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1153 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8669 (m) cc_final: 0.8310 (t) REVERT: M 23 ASP cc_start: 0.6976 (t0) cc_final: 0.6669 (t70) REVERT: M 236 GLU cc_start: 0.5951 (pt0) cc_final: 0.5665 (pt0) REVERT: H 19 SER cc_start: 0.9267 (p) cc_final: 0.9065 (p) REVERT: H 93 SER cc_start: 0.8088 (t) cc_final: 0.7878 (p) REVERT: H 128 HIS cc_start: 0.6873 (m90) cc_final: 0.6611 (m170) REVERT: H 184 LYS cc_start: 0.7216 (mmtp) cc_final: 0.6793 (ttmm) REVERT: H 230 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7750 (mt-10) REVERT: D 5 TYR cc_start: 0.8496 (p90) cc_final: 0.8164 (p90) REVERT: G 9 TYR cc_start: 0.7180 (m-10) cc_final: 0.6975 (m-80) REVERT: K 5 TYR cc_start: 0.7624 (p90) cc_final: 0.7415 (p90) REVERT: K 26 LEU cc_start: 0.8881 (mt) cc_final: 0.8635 (mm) REVERT: O 30 MET cc_start: 0.8060 (ttm) cc_final: 0.7656 (ttm) REVERT: S 3 LYS cc_start: 0.8725 (mttt) cc_final: 0.8491 (mmtm) REVERT: W 8 TRP cc_start: 0.9042 (m100) cc_final: 0.8631 (m100) REVERT: C 25 MET cc_start: 0.8214 (mmm) cc_final: 0.8009 (mmm) REVERT: X 17 THR cc_start: 0.6661 (m) cc_final: 0.6447 (t) REVERT: X 53 ARG cc_start: 0.6628 (mtt-85) cc_final: 0.5483 (ptm160) REVERT: l 48 LEU cc_start: 0.8851 (mt) cc_final: 0.8499 (mt) REVERT: l 52 SER cc_start: 0.8681 (t) cc_final: 0.8446 (m) REVERT: m 23 ASP cc_start: 0.7084 (t0) cc_final: 0.6842 (t70) REVERT: m 36 SER cc_start: 0.8613 (t) cc_final: 0.8394 (t) REVERT: m 233 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7220 (ttp-110) REVERT: m 246 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7850 (mt-10) REVERT: m 272 MET cc_start: 0.8399 (tpp) cc_final: 0.8171 (tpp) REVERT: h 173 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7282 (mp0) REVERT: a 44 LEU cc_start: 0.8996 (mt) cc_final: 0.8714 (mt) REVERT: d 5 TYR cc_start: 0.8493 (p90) cc_final: 0.8119 (p90) REVERT: f 15 ARG cc_start: 0.6707 (mmt90) cc_final: 0.6186 (mtp-110) REVERT: g 9 TYR cc_start: 0.7139 (m-10) cc_final: 0.6919 (m-80) REVERT: k 6 LYS cc_start: 0.8096 (tptt) cc_final: 0.7877 (tptm) REVERT: k 26 LEU cc_start: 0.8923 (mt) cc_final: 0.8643 (mm) REVERT: k 41 TYR cc_start: 0.7328 (m-80) cc_final: 0.7051 (m-80) REVERT: n 28 LEU cc_start: 0.9095 (tp) cc_final: 0.8875 (tp) REVERT: 5 5 TYR cc_start: 0.7992 (p90) cc_final: 0.7369 (p90) REVERT: 4 16 GLN cc_start: 0.7429 (mt0) cc_final: 0.7118 (mm110) REVERT: 6 14 ARG cc_start: 0.6966 (ptm160) cc_final: 0.6558 (ttp-110) REVERT: 6 30 MET cc_start: 0.8144 (ttm) cc_final: 0.7660 (ttm) REVERT: x 28 MET cc_start: 0.7010 (ttm) cc_final: 0.6728 (tpt) REVERT: x 53 ARG cc_start: 0.6363 (mtt-85) cc_final: 0.5388 (ptm160) REVERT: y 6 GLU cc_start: 0.6869 (tp30) cc_final: 0.6561 (tp30) outliers start: 14 outliers final: 10 residues processed: 1160 average time/residue: 0.6022 time to fit residues: 896.1030 Evaluate side-chains 862 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 852 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain b1 residue 29 VAL Chi-restraints excluded: chain b0 residue 40 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 199 ASN H 35 ASN H 194 GLN D 20 GLN I 20 GLN V 18 GLN 3 20 GLN Z 18 GLN 7 20 GLN l 199 ASN h 194 GLN h 199 GLN i 20 GLN k 42 ASN k 52 ASN n 18 GLN q 52 ASN r 16 GLN ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 18 GLN z 16 GLN ** z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN x 26 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.110863 restraints weight = 65251.320| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.09 r_work: 0.3103 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 46764 Z= 0.282 Angle : 0.737 11.380 64138 Z= 0.321 Chirality : 0.042 0.228 6216 Planarity : 0.004 0.051 7888 Dihedral : 16.782 179.933 8473 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.78 % Allowed : 13.24 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.12), residues: 4462 helix: 2.08 (0.09), residues: 2922 sheet: -0.83 (0.78), residues: 48 loop : 0.32 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 118 TYR 0.018 0.002 TYR a 41 PHE 0.021 0.002 PHE L 216 TRP 0.017 0.002 TRP o 8 HIS 0.012 0.002 HIS z 21 Details of bonding type rmsd covalent geometry : bond 0.00660 (46700) covalent geometry : angle 0.73661 (64138) hydrogen bonds : bond 0.05526 ( 2564) hydrogen bonds : angle 4.33286 ( 7407) Misc. bond : bond 0.00360 ( 64) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 959 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 17 ASP cc_start: 0.7737 (t0) cc_final: 0.7300 (m-30) REVERT: M 21 THR cc_start: 0.8954 (m) cc_final: 0.8541 (t) REVERT: M 23 ASP cc_start: 0.7423 (t0) cc_final: 0.7120 (t70) REVERT: M 36 SER cc_start: 0.8930 (t) cc_final: 0.8670 (t) REVERT: M 240 ASP cc_start: 0.7221 (m-30) cc_final: 0.7003 (p0) REVERT: H 18 TYR cc_start: 0.9119 (m-80) cc_final: 0.8896 (m-80) REVERT: H 163 LYS cc_start: 0.8825 (pttt) cc_final: 0.8551 (ptmm) REVERT: H 184 LYS cc_start: 0.7255 (mmtp) cc_final: 0.6716 (ttmm) REVERT: A 9 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8407 (mmm) REVERT: D 5 TYR cc_start: 0.8701 (p90) cc_final: 0.8323 (p90) REVERT: E 7 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7595 (pp) REVERT: F 15 ARG cc_start: 0.7118 (mmt90) cc_final: 0.6172 (mtp-110) REVERT: G 9 TYR cc_start: 0.7410 (m-10) cc_final: 0.7199 (m-80) REVERT: I 3 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8126 (mtmm) REVERT: I 5 TYR cc_start: 0.8056 (p90) cc_final: 0.7793 (p90) REVERT: I 9 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7539 (mtm) REVERT: K 3 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8024 (tmtp) REVERT: K 5 TYR cc_start: 0.7779 (p90) cc_final: 0.7362 (p90) REVERT: K 41 TYR cc_start: 0.7507 (m-80) cc_final: 0.7066 (m-80) REVERT: N 18 GLN cc_start: 0.7475 (mt0) cc_final: 0.7135 (tp-100) REVERT: O 3 LYS cc_start: 0.8084 (ttmm) cc_final: 0.7407 (tptp) REVERT: O 17 PHE cc_start: 0.8825 (m-80) cc_final: 0.8547 (m-80) REVERT: O 30 MET cc_start: 0.8850 (ttm) cc_final: 0.8641 (ttm) REVERT: P 13 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7782 (t) REVERT: S 3 LYS cc_start: 0.9041 (mttt) cc_final: 0.8560 (mmtm) REVERT: U 15 ARG cc_start: 0.8174 (mmt90) cc_final: 0.6994 (mtm110) REVERT: V 15 GLU cc_start: 0.7956 (mp0) cc_final: 0.7542 (tm-30) REVERT: W 41 TYR cc_start: 0.7436 (m-80) cc_final: 0.7191 (m-80) REVERT: 3 7 ILE cc_start: 0.8294 (tp) cc_final: 0.8040 (pt) REVERT: 1 45 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7816 (tp30) REVERT: 8 14 ASP cc_start: 0.7843 (m-30) cc_final: 0.7519 (t70) REVERT: X 28 MET cc_start: 0.6772 (tmm) cc_final: 0.6485 (tmm) REVERT: X 53 ARG cc_start: 0.6615 (mtt-85) cc_final: 0.5156 (ptm160) REVERT: l 213 ASP cc_start: 0.8043 (m-30) cc_final: 0.7763 (m-30) REVERT: m 21 THR cc_start: 0.8938 (m) cc_final: 0.8508 (t) REVERT: m 23 ASP cc_start: 0.7409 (t0) cc_final: 0.6968 (t0) REVERT: m 36 SER cc_start: 0.8958 (t) cc_final: 0.8703 (t) REVERT: m 184 ASP cc_start: 0.8121 (m-30) cc_final: 0.7896 (m-30) REVERT: m 218 MET cc_start: 0.8705 (mtp) cc_final: 0.8493 (mtm) REVERT: m 233 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7267 (ttm110) REVERT: h 18 TYR cc_start: 0.9130 (m-80) cc_final: 0.8890 (m-80) REVERT: h 170 ASP cc_start: 0.7933 (t0) cc_final: 0.7087 (t70) REVERT: h 173 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7331 (mp0) REVERT: h 206 ASN cc_start: 0.7769 (t0) cc_final: 0.7527 (t0) REVERT: h 231 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8078 (t0) REVERT: a 38 THR cc_start: 0.7544 (p) cc_final: 0.7344 (t) REVERT: d 5 TYR cc_start: 0.8827 (p90) cc_final: 0.8605 (p90) REVERT: e 18 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: f 15 ARG cc_start: 0.7232 (mmt90) cc_final: 0.6300 (mtp-110) REVERT: g 19 GLU cc_start: 0.8157 (tt0) cc_final: 0.7949 (tt0) REVERT: i 3 LYS cc_start: 0.8555 (mtpm) cc_final: 0.8214 (mtmm) REVERT: i 5 TYR cc_start: 0.8081 (p90) cc_final: 0.7691 (p90) REVERT: j 32 SER cc_start: 0.8969 (p) cc_final: 0.8688 (m) REVERT: k 3 LYS cc_start: 0.8328 (tmtp) cc_final: 0.7955 (tmtp) REVERT: k 6 LYS cc_start: 0.7920 (tptt) cc_final: 0.7719 (tptm) REVERT: k 41 TYR cc_start: 0.7683 (m-80) cc_final: 0.7349 (m-80) REVERT: o 3 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7491 (mtpp) REVERT: q 45 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: s 1 MET cc_start: 0.4499 (OUTLIER) cc_final: 0.4230 (tmt) REVERT: s 46 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7876 (mp) REVERT: t 23 VAL cc_start: 0.8903 (t) cc_final: 0.8549 (p) REVERT: u 15 ARG cc_start: 0.8058 (mmt90) cc_final: 0.7602 (mtt90) REVERT: v 14 ASP cc_start: 0.7797 (t0) cc_final: 0.7479 (t0) REVERT: 5 5 TYR cc_start: 0.8073 (p90) cc_final: 0.7249 (p90) REVERT: b1 6 LYS cc_start: 0.7376 (mmtt) cc_final: 0.7135 (mmtp) REVERT: 4 16 GLN cc_start: 0.7532 (mt0) cc_final: 0.7107 (mm110) REVERT: 4 25 MET cc_start: 0.7143 (mmm) cc_final: 0.6862 (ttm) REVERT: x 53 ARG cc_start: 0.6336 (mtt-85) cc_final: 0.5158 (ptm160) REVERT: y 6 GLU cc_start: 0.7319 (tp30) cc_final: 0.7079 (tp30) outliers start: 144 outliers final: 48 residues processed: 1017 average time/residue: 0.5887 time to fit residues: 772.7942 Evaluate side-chains 916 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 857 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain I residue 9 MET Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 46 ILE Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 159 VAL Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 45 GLU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 46 ILE Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain z residue 42 VAL Chi-restraints excluded: chain b1 residue 20 GLN Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 4 residue 46 ARG Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b8 residue 40 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 70 optimal weight: 0.4980 chunk 134 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 407 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 350 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN I 20 GLN P 16 GLN ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 20 GLN Z 18 GLN 7 20 GLN 0 16 GLN X 26 GLN Y 51 ASN l 199 ASN h 35 ASN ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 194 GLN k 52 ASN n 16 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 16 GLN r 16 GLN ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 16 GLN 4 18 GLN 6 20 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.137889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.112525 restraints weight = 65013.030| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.34 r_work: 0.3120 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 46764 Z= 0.172 Angle : 0.635 11.417 64138 Z= 0.276 Chirality : 0.039 0.145 6216 Planarity : 0.004 0.041 7888 Dihedral : 16.304 179.982 8468 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.73 % Allowed : 15.86 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.12), residues: 4462 helix: 2.17 (0.09), residues: 2928 sheet: -0.84 (0.76), residues: 48 loop : 0.31 (0.17), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG s 14 TYR 0.017 0.001 TYR 2 24 PHE 0.021 0.001 PHE 5 23 TRP 0.014 0.001 TRP j 48 HIS 0.013 0.001 HIS Z 21 Details of bonding type rmsd covalent geometry : bond 0.00396 (46700) covalent geometry : angle 0.63522 (64138) hydrogen bonds : bond 0.05031 ( 2564) hydrogen bonds : angle 4.15544 ( 7407) Misc. bond : bond 0.00279 ( 64) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 956 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 201 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: L 257 ASP cc_start: 0.8360 (m-30) cc_final: 0.8085 (t0) REVERT: M 17 ASP cc_start: 0.7907 (t0) cc_final: 0.7428 (m-30) REVERT: M 21 THR cc_start: 0.8866 (m) cc_final: 0.8417 (t) REVERT: M 23 ASP cc_start: 0.7409 (t0) cc_final: 0.6939 (t70) REVERT: M 36 SER cc_start: 0.8896 (t) cc_final: 0.8652 (t) REVERT: M 122 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8653 (ttt) REVERT: H 163 LYS cc_start: 0.8895 (pttt) cc_final: 0.8636 (ptmm) REVERT: H 184 LYS cc_start: 0.7087 (mmtp) cc_final: 0.6482 (ttmm) REVERT: A 5 TYR cc_start: 0.9136 (p90) cc_final: 0.8858 (p90) REVERT: A 12 ASP cc_start: 0.8672 (t70) cc_final: 0.8368 (t0) REVERT: D 5 TYR cc_start: 0.8821 (p90) cc_final: 0.8472 (p90) REVERT: E 18 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: F 1 MET cc_start: 0.6959 (mmm) cc_final: 0.6742 (mmm) REVERT: F 15 ARG cc_start: 0.7085 (mmt90) cc_final: 0.6211 (mtp-110) REVERT: G 19 GLU cc_start: 0.8111 (tt0) cc_final: 0.7897 (tt0) REVERT: I 5 TYR cc_start: 0.8130 (p90) cc_final: 0.7788 (p90) REVERT: J 28 LEU cc_start: 0.9206 (tt) cc_final: 0.8953 (tp) REVERT: K 3 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8235 (tmtp) REVERT: K 5 TYR cc_start: 0.7848 (p90) cc_final: 0.7440 (p90) REVERT: K 6 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7484 (tptp) REVERT: N 16 GLN cc_start: 0.7701 (mt0) cc_final: 0.7394 (mt0) REVERT: N 18 GLN cc_start: 0.7606 (mt0) cc_final: 0.7397 (tp-100) REVERT: O 3 LYS cc_start: 0.7917 (ttmm) cc_final: 0.7239 (tptp) REVERT: P 13 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7855 (t) REVERT: Q 45 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7591 (tm-30) REVERT: S 3 LYS cc_start: 0.9054 (mttt) cc_final: 0.8576 (mmtm) REVERT: U 15 ARG cc_start: 0.8133 (mmt90) cc_final: 0.7093 (mtm110) REVERT: W 9 MET cc_start: 0.8639 (mtp) cc_final: 0.8420 (mmt) REVERT: W 37 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8368 (p) REVERT: 3 7 ILE cc_start: 0.8339 (tp) cc_final: 0.8091 (pt) REVERT: 2 25 MET cc_start: 0.7646 (mmm) cc_final: 0.7414 (mmm) REVERT: 8 14 ASP cc_start: 0.7815 (m-30) cc_final: 0.7532 (t70) REVERT: X 17 THR cc_start: 0.6736 (m) cc_final: 0.6097 (t) REVERT: X 28 MET cc_start: 0.6749 (tmm) cc_final: 0.6381 (tmm) REVERT: X 53 ARG cc_start: 0.6637 (mtt-85) cc_final: 0.5164 (ptm160) REVERT: Y 51 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.6748 (t0) REVERT: l 20 ASN cc_start: 0.8239 (p0) cc_final: 0.8011 (p0) REVERT: l 52 SER cc_start: 0.8676 (t) cc_final: 0.8466 (m) REVERT: l 213 ASP cc_start: 0.8062 (m-30) cc_final: 0.7786 (m-30) REVERT: m 21 THR cc_start: 0.8815 (m) cc_final: 0.8380 (t) REVERT: m 23 ASP cc_start: 0.7416 (t0) cc_final: 0.6912 (t0) REVERT: m 36 SER cc_start: 0.8980 (t) cc_final: 0.8744 (t) REVERT: m 122 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8621 (ttt) REVERT: m 233 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7162 (ttm110) REVERT: h 173 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7625 (mp0) REVERT: h 175 MET cc_start: 0.8282 (ptp) cc_final: 0.8027 (ptp) REVERT: h 206 ASN cc_start: 0.7694 (t0) cc_final: 0.6852 (t0) REVERT: h 231 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8131 (t0) REVERT: a 38 THR cc_start: 0.7580 (p) cc_final: 0.7347 (t) REVERT: d 5 TYR cc_start: 0.8812 (p90) cc_final: 0.8588 (p90) REVERT: e 18 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: f 9 MET cc_start: 0.7669 (mmm) cc_final: 0.7365 (mmp) REVERT: f 15 ARG cc_start: 0.7288 (mmt90) cc_final: 0.6399 (mtp-110) REVERT: g 19 GLU cc_start: 0.8155 (tt0) cc_final: 0.7917 (tt0) REVERT: i 5 TYR cc_start: 0.8039 (p90) cc_final: 0.7621 (p90) REVERT: j 32 SER cc_start: 0.8972 (p) cc_final: 0.8741 (m) REVERT: k 3 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7721 (tmtp) REVERT: k 6 LYS cc_start: 0.7892 (tptt) cc_final: 0.7585 (tptm) REVERT: k 41 TYR cc_start: 0.7617 (m-80) cc_final: 0.7115 (m-80) REVERT: o 3 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7526 (mtpp) REVERT: o 6 LYS cc_start: 0.7512 (mtpt) cc_final: 0.7162 (mmmt) REVERT: o 8 TRP cc_start: 0.8482 (m100) cc_final: 0.8272 (m100) REVERT: p 25 MET cc_start: 0.8814 (mmm) cc_final: 0.8588 (mpp) REVERT: q 45 GLU cc_start: 0.8366 (tp30) cc_final: 0.7599 (tm-30) REVERT: s 1 MET cc_start: 0.4450 (OUTLIER) cc_final: 0.4092 (tmt) REVERT: s 14 ARG cc_start: 0.8330 (mtm110) cc_final: 0.7900 (mtm180) REVERT: t 19 GLU cc_start: 0.7717 (pt0) cc_final: 0.6960 (pt0) REVERT: t 20 LEU cc_start: 0.9018 (tt) cc_final: 0.8794 (tp) REVERT: t 23 VAL cc_start: 0.8920 (t) cc_final: 0.8660 (p) REVERT: u 15 ARG cc_start: 0.8106 (mmt90) cc_final: 0.7592 (mtt90) REVERT: v 16 GLN cc_start: 0.8392 (mt0) cc_final: 0.8119 (mt0) REVERT: w 37 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8411 (p) REVERT: c 9 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7353 (m-10) REVERT: 5 3 LYS cc_start: 0.7734 (mmmt) cc_final: 0.7291 (ttmm) REVERT: 5 5 TYR cc_start: 0.7950 (p90) cc_final: 0.7236 (p90) REVERT: b1 6 LYS cc_start: 0.7549 (mmtt) cc_final: 0.7305 (mmtp) REVERT: 4 16 GLN cc_start: 0.7497 (mt0) cc_final: 0.7087 (mm110) REVERT: b8 15 GLU cc_start: 0.8001 (mp0) cc_final: 0.7750 (pm20) REVERT: x 28 MET cc_start: 0.7779 (mtm) cc_final: 0.7086 (tmt) REVERT: x 53 ARG cc_start: 0.6359 (mtt-85) cc_final: 0.5019 (ptm160) REVERT: y 6 GLU cc_start: 0.7415 (tp30) cc_final: 0.6313 (pm20) REVERT: y 36 LEU cc_start: 0.8496 (tp) cc_final: 0.8208 (tm) outliers start: 142 outliers final: 51 residues processed: 1024 average time/residue: 0.4795 time to fit residues: 635.2821 Evaluate side-chains 957 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 891 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain 3 residue 27 LEU Chi-restraints excluded: chain 1 residue 20 GLN Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain l residue 46 ILE Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain m residue 122 MET Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b0 residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 97 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 342 optimal weight: 10.0000 chunk 385 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 430 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN I 20 GLN K 42 ASN P 16 GLN Q 20 GLN ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 18 GLN ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 199 ASN h 194 GLN i 20 GLN k 42 ASN k 52 ASN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 GLN b1 20 GLN 4 18 GLN 6 20 GLN x 18 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108553 restraints weight = 65105.021| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.09 r_work: 0.3077 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 46764 Z= 0.307 Angle : 0.779 11.103 64138 Z= 0.331 Chirality : 0.043 0.169 6216 Planarity : 0.004 0.090 7888 Dihedral : 16.790 179.887 8464 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.36 % Allowed : 17.07 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.12), residues: 4462 helix: 1.84 (0.09), residues: 2906 sheet: -1.14 (0.74), residues: 48 loop : 0.13 (0.17), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 247 TYR 0.022 0.002 TYR s 41 PHE 0.023 0.002 PHE l 216 TRP 0.017 0.002 TRP j 48 HIS 0.014 0.002 HIS Z 21 Details of bonding type rmsd covalent geometry : bond 0.00730 (46700) covalent geometry : angle 0.77931 (64138) hydrogen bonds : bond 0.05274 ( 2564) hydrogen bonds : angle 4.29368 ( 7407) Misc. bond : bond 0.00445 ( 64) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 920 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 257 ASP cc_start: 0.8247 (m-30) cc_final: 0.8030 (t70) REVERT: M 17 ASP cc_start: 0.7939 (t0) cc_final: 0.7538 (m-30) REVERT: M 21 THR cc_start: 0.8975 (m) cc_final: 0.8504 (t) REVERT: M 23 ASP cc_start: 0.7416 (t0) cc_final: 0.6944 (t0) REVERT: M 36 SER cc_start: 0.8944 (t) cc_final: 0.8693 (t) REVERT: H 163 LYS cc_start: 0.8933 (pttt) cc_final: 0.8682 (ptmm) REVERT: H 175 MET cc_start: 0.8224 (ptp) cc_final: 0.8015 (ptp) REVERT: H 184 LYS cc_start: 0.7015 (mmtp) cc_final: 0.6389 (ttmm) REVERT: A 12 ASP cc_start: 0.8816 (t70) cc_final: 0.8539 (t0) REVERT: D 5 TYR cc_start: 0.8840 (p90) cc_final: 0.8446 (p90) REVERT: E 18 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: F 9 MET cc_start: 0.7777 (mmm) cc_final: 0.7483 (mmp) REVERT: F 15 ARG cc_start: 0.7261 (mmt90) cc_final: 0.6355 (mtp-110) REVERT: G 30 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8755 (tp) REVERT: I 3 LYS cc_start: 0.8527 (mtpm) cc_final: 0.8018 (tppp) REVERT: I 5 TYR cc_start: 0.8141 (p90) cc_final: 0.7858 (p90) REVERT: K 5 TYR cc_start: 0.7883 (p90) cc_final: 0.7521 (p90) REVERT: N 16 GLN cc_start: 0.7683 (mt0) cc_final: 0.7374 (mt0) REVERT: O 3 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7549 (tmtt) REVERT: O 45 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7212 (mm-30) REVERT: Q 6 LYS cc_start: 0.8632 (tptm) cc_final: 0.8426 (tppp) REVERT: Q 41 TYR cc_start: 0.8272 (m-80) cc_final: 0.8015 (m-80) REVERT: Q 45 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7648 (tm-30) REVERT: S 3 LYS cc_start: 0.9080 (mttt) cc_final: 0.8607 (mmtm) REVERT: T 23 VAL cc_start: 0.9019 (t) cc_final: 0.8774 (p) REVERT: U 15 ARG cc_start: 0.8178 (mmt90) cc_final: 0.7037 (mtm110) REVERT: V 14 ASP cc_start: 0.7795 (t0) cc_final: 0.7278 (t0) REVERT: W 41 TYR cc_start: 0.7596 (m-80) cc_final: 0.7369 (m-80) REVERT: C 25 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8431 (mmm) REVERT: 3 7 ILE cc_start: 0.8539 (tp) cc_final: 0.8258 (pt) REVERT: 1 26 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8434 (mp) REVERT: 2 15 GLU cc_start: 0.6991 (pm20) cc_final: 0.6585 (pm20) REVERT: 8 14 ASP cc_start: 0.7866 (m-30) cc_final: 0.7617 (t70) REVERT: 0 16 GLN cc_start: 0.8867 (mt0) cc_final: 0.8572 (mt0) REVERT: 0 19 GLU cc_start: 0.8631 (tt0) cc_final: 0.8355 (tm-30) REVERT: X 17 THR cc_start: 0.6800 (m) cc_final: 0.6118 (t) REVERT: X 53 ARG cc_start: 0.6505 (mtt-85) cc_final: 0.5396 (ptm160) REVERT: Y 6 GLU cc_start: 0.7343 (tp30) cc_final: 0.6572 (pm20) REVERT: l 213 ASP cc_start: 0.8100 (m-30) cc_final: 0.7870 (m-30) REVERT: m 21 THR cc_start: 0.9006 (m) cc_final: 0.8547 (t) REVERT: m 23 ASP cc_start: 0.7528 (t0) cc_final: 0.6887 (t0) REVERT: m 36 SER cc_start: 0.9005 (t) cc_final: 0.8742 (t) REVERT: m 122 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8696 (ttt) REVERT: m 233 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7248 (mtm-85) REVERT: h 173 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7668 (mp0) REVERT: h 175 MET cc_start: 0.8287 (ptp) cc_final: 0.8059 (ptp) REVERT: h 231 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8095 (t0) REVERT: a 38 THR cc_start: 0.7654 (p) cc_final: 0.7446 (t) REVERT: d 3 LYS cc_start: 0.8820 (mttt) cc_final: 0.8544 (mtpt) REVERT: d 5 TYR cc_start: 0.8861 (p90) cc_final: 0.8578 (p90) REVERT: e 18 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: f 9 MET cc_start: 0.7850 (mmm) cc_final: 0.7532 (mmp) REVERT: f 15 ARG cc_start: 0.7323 (mmt90) cc_final: 0.6401 (mtp-110) REVERT: g 19 GLU cc_start: 0.8106 (tt0) cc_final: 0.7864 (tt0) REVERT: i 3 LYS cc_start: 0.8608 (mtpm) cc_final: 0.8077 (tppp) REVERT: i 5 TYR cc_start: 0.8029 (p90) cc_final: 0.7660 (p90) REVERT: j 32 SER cc_start: 0.9071 (p) cc_final: 0.8841 (m) REVERT: k 3 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7879 (tmtp) REVERT: k 41 TYR cc_start: 0.7792 (m-80) cc_final: 0.7467 (m-80) REVERT: o 3 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7613 (mtpp) REVERT: o 6 LYS cc_start: 0.7568 (mtpt) cc_final: 0.7218 (mmmt) REVERT: q 45 GLU cc_start: 0.8262 (tp30) cc_final: 0.7519 (tm-30) REVERT: s 14 ARG cc_start: 0.8408 (mtm110) cc_final: 0.7973 (mtm180) REVERT: t 20 LEU cc_start: 0.9037 (tt) cc_final: 0.8762 (tp) REVERT: t 23 VAL cc_start: 0.8895 (t) cc_final: 0.8692 (p) REVERT: u 15 ARG cc_start: 0.8088 (mmt90) cc_final: 0.7553 (mtt90) REVERT: v 14 ASP cc_start: 0.7908 (t70) cc_final: 0.7446 (t0) REVERT: w 41 TYR cc_start: 0.7662 (m-80) cc_final: 0.7387 (m-80) REVERT: 5 3 LYS cc_start: 0.7686 (mmmt) cc_final: 0.7283 (ttmm) REVERT: 5 5 TYR cc_start: 0.8092 (p90) cc_final: 0.7524 (p90) REVERT: 5 14 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7179 (mtm180) REVERT: 4 16 GLN cc_start: 0.7523 (mt0) cc_final: 0.7120 (mp-120) REVERT: 4 46 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7989 (mtp85) REVERT: b9 3 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8671 (mmmm) REVERT: b9 10 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8647 (mt) REVERT: x 28 MET cc_start: 0.7782 (mtm) cc_final: 0.7220 (tmm) REVERT: x 53 ARG cc_start: 0.6434 (mtt-85) cc_final: 0.5280 (ptm160) REVERT: y 6 GLU cc_start: 0.7380 (tp30) cc_final: 0.6325 (pm20) REVERT: y 36 LEU cc_start: 0.8393 (tp) cc_final: 0.8163 (tm) outliers start: 166 outliers final: 70 residues processed: 991 average time/residue: 0.4024 time to fit residues: 517.8484 Evaluate side-chains 957 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 875 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 1 residue 20 GLN Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 0 residue 18 GLN Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 122 MET Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain 5 residue 14 ARG Chi-restraints excluded: chain z residue 42 VAL Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 5 TYR Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 46 ARG Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b8 residue 40 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 3 LYS Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 221 optimal weight: 0.6980 chunk 366 optimal weight: 0.8980 chunk 384 optimal weight: 0.8980 chunk 326 optimal weight: 0.9980 chunk 422 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 410 optimal weight: 0.8980 chunk 392 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN K 42 ASN N 18 GLN Q 20 GLN S 20 GLN W 20 GLN 3 20 GLN 7 20 GLN Y 51 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 16 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 20 GLN x 18 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112953 restraints weight = 64519.924| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.13 r_work: 0.3143 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 46764 Z= 0.146 Angle : 0.628 11.061 64138 Z= 0.274 Chirality : 0.038 0.173 6216 Planarity : 0.003 0.045 7888 Dihedral : 16.191 179.951 8464 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.99 % Allowed : 20.33 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.12), residues: 4462 helix: 2.16 (0.09), residues: 2930 sheet: -0.98 (0.74), residues: 48 loop : 0.16 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 233 TYR 0.015 0.001 TYRb9 41 PHE 0.024 0.001 PHE 3 23 TRP 0.014 0.001 TRP o 8 HIS 0.012 0.001 HIS Z 21 Details of bonding type rmsd covalent geometry : bond 0.00334 (46700) covalent geometry : angle 0.62849 (64138) hydrogen bonds : bond 0.04790 ( 2564) hydrogen bonds : angle 4.08746 ( 7407) Misc. bond : bond 0.00212 ( 64) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 990 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 201 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: L 257 ASP cc_start: 0.8289 (m-30) cc_final: 0.8056 (t0) REVERT: M 17 ASP cc_start: 0.8016 (t0) cc_final: 0.7620 (m-30) REVERT: M 21 THR cc_start: 0.8738 (m) cc_final: 0.8198 (t) REVERT: M 23 ASP cc_start: 0.7259 (t0) cc_final: 0.6862 (t0) REVERT: M 36 SER cc_start: 0.8969 (t) cc_final: 0.8630 (p) REVERT: H 128 HIS cc_start: 0.8081 (m-70) cc_final: 0.7700 (m170) REVERT: H 163 LYS cc_start: 0.8910 (pttt) cc_final: 0.8660 (ptmm) REVERT: H 184 LYS cc_start: 0.6975 (mmtp) cc_final: 0.6339 (ttmm) REVERT: A 12 ASP cc_start: 0.8751 (t70) cc_final: 0.8432 (t0) REVERT: D 3 LYS cc_start: 0.8733 (mttt) cc_final: 0.8503 (mtpt) REVERT: D 5 TYR cc_start: 0.8806 (p90) cc_final: 0.8461 (p90) REVERT: E 18 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7943 (mt0) REVERT: F 9 MET cc_start: 0.7708 (mmm) cc_final: 0.7453 (mmp) REVERT: F 10 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7540 (mt) REVERT: F 15 ARG cc_start: 0.7220 (mmt90) cc_final: 0.6340 (mtp-110) REVERT: G 19 GLU cc_start: 0.8140 (tt0) cc_final: 0.7907 (tt0) REVERT: I 3 LYS cc_start: 0.8450 (mtpm) cc_final: 0.7992 (tppp) REVERT: I 5 TYR cc_start: 0.8202 (p90) cc_final: 0.7901 (p90) REVERT: I 54 VAL cc_start: 0.8287 (t) cc_final: 0.8077 (p) REVERT: K 5 TYR cc_start: 0.7882 (p90) cc_final: 0.7585 (p90) REVERT: K 6 LYS cc_start: 0.7902 (tptm) cc_final: 0.7551 (tptp) REVERT: N 16 GLN cc_start: 0.7678 (mt0) cc_final: 0.7366 (mt0) REVERT: O 1 MET cc_start: 0.4207 (tmt) cc_final: 0.3983 (tmm) REVERT: O 3 LYS cc_start: 0.8012 (ttmm) cc_final: 0.7379 (tmtt) REVERT: O 45 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7136 (mm-30) REVERT: Q 6 LYS cc_start: 0.8560 (tptm) cc_final: 0.8106 (tppp) REVERT: Q 45 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7687 (tm-30) REVERT: S 3 LYS cc_start: 0.9067 (mttt) cc_final: 0.8588 (mmtm) REVERT: U 15 ARG cc_start: 0.8133 (mmt90) cc_final: 0.7090 (mtm110) REVERT: W 6 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8517 (mtmm) REVERT: W 9 MET cc_start: 0.8652 (mtp) cc_final: 0.8384 (mmt) REVERT: W 37 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8361 (p) REVERT: C 9 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: 3 7 ILE cc_start: 0.8414 (tp) cc_final: 0.8207 (pt) REVERT: 1 45 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8040 (tp30) REVERT: 2 25 MET cc_start: 0.7648 (mmm) cc_final: 0.7411 (mmm) REVERT: 9 10 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8638 (mt) REVERT: 0 19 GLU cc_start: 0.8577 (tt0) cc_final: 0.8316 (tm-30) REVERT: X 17 THR cc_start: 0.6734 (m) cc_final: 0.6063 (t) REVERT: X 28 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6467 (tmm) REVERT: X 53 ARG cc_start: 0.6405 (mtt-85) cc_final: 0.5245 (ptm160) REVERT: Y 6 GLU cc_start: 0.7319 (tp30) cc_final: 0.6965 (tp30) REVERT: Y 10 ARG cc_start: 0.7573 (tpt90) cc_final: 0.7304 (mtt-85) REVERT: m 17 ASP cc_start: 0.8063 (t0) cc_final: 0.7566 (m-30) REVERT: m 21 THR cc_start: 0.8810 (m) cc_final: 0.8352 (t) REVERT: m 23 ASP cc_start: 0.7361 (t0) cc_final: 0.6936 (t0) REVERT: m 122 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8575 (ttt) REVERT: m 233 ARG cc_start: 0.7557 (mtm-85) cc_final: 0.7210 (mtm180) REVERT: h 173 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7582 (mp0) REVERT: h 175 MET cc_start: 0.8210 (ptp) cc_final: 0.8008 (ptp) REVERT: h 231 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8093 (t0) REVERT: a 9 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8528 (mtm) REVERT: d 3 LYS cc_start: 0.8764 (mttt) cc_final: 0.8534 (mtpt) REVERT: d 5 TYR cc_start: 0.8837 (p90) cc_final: 0.8501 (p90) REVERT: e 18 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: f 9 MET cc_start: 0.7773 (mmm) cc_final: 0.7441 (mmp) REVERT: f 10 ILE cc_start: 0.7712 (mm) cc_final: 0.7462 (mt) REVERT: f 15 ARG cc_start: 0.7159 (mmt90) cc_final: 0.6321 (mtp-110) REVERT: g 19 GLU cc_start: 0.8099 (tt0) cc_final: 0.7880 (tt0) REVERT: i 3 LYS cc_start: 0.8589 (mtpm) cc_final: 0.8036 (tppp) REVERT: i 5 TYR cc_start: 0.7982 (p90) cc_final: 0.7481 (p90) REVERT: k 3 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7922 (tmtp) REVERT: n 28 LEU cc_start: 0.8870 (tt) cc_final: 0.8641 (tp) REVERT: o 3 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7661 (mtpp) REVERT: o 6 LYS cc_start: 0.7554 (mtpt) cc_final: 0.7210 (mmmt) REVERT: q 45 GLU cc_start: 0.8276 (tp30) cc_final: 0.7615 (tm-30) REVERT: s 14 ARG cc_start: 0.8421 (mtm110) cc_final: 0.8198 (mtt90) REVERT: t 14 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7524 (t0) REVERT: t 16 GLN cc_start: 0.8349 (mt0) cc_final: 0.7699 (mp10) REVERT: u 15 ARG cc_start: 0.8054 (mmt90) cc_final: 0.7584 (mtt90) REVERT: w 37 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8397 (p) REVERT: c 9 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7412 (m-10) REVERT: 5 5 TYR cc_start: 0.7983 (p90) cc_final: 0.7369 (p90) REVERT: b1 4 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.6007 (m-10) REVERT: b1 5 TYR cc_start: 0.6938 (p90) cc_final: 0.5987 (p90) REVERT: b1 6 LYS cc_start: 0.7375 (mmtt) cc_final: 0.7154 (mmtp) REVERT: b1 37 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8446 (p) REVERT: 4 15 GLU cc_start: 0.7936 (pt0) cc_final: 0.7567 (pm20) REVERT: 4 16 GLN cc_start: 0.7601 (mt0) cc_final: 0.7243 (mp-120) REVERT: b8 15 GLU cc_start: 0.7957 (mp0) cc_final: 0.7733 (pm20) REVERT: b9 10 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8608 (mt) REVERT: x 28 MET cc_start: 0.7672 (mtm) cc_final: 0.7072 (tmt) REVERT: x 53 ARG cc_start: 0.6382 (mtt-85) cc_final: 0.5236 (ptm160) REVERT: y 6 GLU cc_start: 0.7378 (tp30) cc_final: 0.6322 (pm20) REVERT: y 36 LEU cc_start: 0.8431 (tp) cc_final: 0.8165 (tm) outliers start: 114 outliers final: 42 residues processed: 1040 average time/residue: 0.3594 time to fit residues: 487.7759 Evaluate side-chains 968 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 907 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain C residue 9 TYR Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain m residue 122 MET Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 9 MET Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain t residue 14 ASP Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 435 optimal weight: 0.8980 chunk 401 optimal weight: 2.9990 chunk 281 optimal weight: 0.4980 chunk 375 optimal weight: 0.8980 chunk 379 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 191 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 374 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN K 42 ASN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 16 GLN Y 51 ASN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN k 42 ASN n 16 GLN o 20 GLN b1 20 GLN x 18 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.138028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112711 restraints weight = 64668.298| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.14 r_work: 0.3143 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 46764 Z= 0.154 Angle : 0.642 11.030 64138 Z= 0.279 Chirality : 0.038 0.193 6216 Planarity : 0.003 0.045 7888 Dihedral : 15.982 179.947 8464 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.68 % Allowed : 21.11 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.12), residues: 4462 helix: 2.22 (0.09), residues: 2938 sheet: -0.79 (0.75), residues: 48 loop : 0.17 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 233 TYR 0.020 0.001 TYR m 76 PHE 0.024 0.001 PHE 3 23 TRP 0.013 0.001 TRP Z 29 HIS 0.013 0.001 HIS Z 21 Details of bonding type rmsd covalent geometry : bond 0.00354 (46700) covalent geometry : angle 0.64157 (64138) hydrogen bonds : bond 0.04731 ( 2564) hydrogen bonds : angle 4.06156 ( 7407) Misc. bond : bond 0.00236 ( 64) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 949 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 201 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: L 257 ASP cc_start: 0.8285 (m-30) cc_final: 0.8047 (t0) REVERT: M 17 ASP cc_start: 0.8000 (t0) cc_final: 0.7612 (m-30) REVERT: M 21 THR cc_start: 0.8814 (m) cc_final: 0.8235 (t) REVERT: M 23 ASP cc_start: 0.7284 (t0) cc_final: 0.6796 (t0) REVERT: M 36 SER cc_start: 0.8956 (t) cc_final: 0.8587 (p) REVERT: M 60 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8129 (mp) REVERT: M 122 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8550 (ttt) REVERT: M 233 ARG cc_start: 0.7419 (ttp-110) cc_final: 0.7043 (ttp-110) REVERT: H 163 LYS cc_start: 0.8902 (pttt) cc_final: 0.8664 (ptmm) REVERT: H 184 LYS cc_start: 0.6957 (mmtp) cc_final: 0.6339 (ttmm) REVERT: H 226 THR cc_start: 0.8627 (p) cc_final: 0.8100 (t) REVERT: A 12 ASP cc_start: 0.8703 (t70) cc_final: 0.8397 (t0) REVERT: D 3 LYS cc_start: 0.8764 (mttt) cc_final: 0.8539 (mtpt) REVERT: D 5 TYR cc_start: 0.8820 (p90) cc_final: 0.8513 (p90) REVERT: F 9 MET cc_start: 0.7709 (mmm) cc_final: 0.7454 (mmp) REVERT: F 10 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7523 (mt) REVERT: F 15 ARG cc_start: 0.7225 (mmt90) cc_final: 0.6369 (mtp-110) REVERT: G 12 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7623 (mp) REVERT: G 19 GLU cc_start: 0.8125 (tt0) cc_final: 0.7888 (tt0) REVERT: I 3 LYS cc_start: 0.8452 (mtpm) cc_final: 0.7999 (tppp) REVERT: I 5 TYR cc_start: 0.8215 (p90) cc_final: 0.7967 (p90) REVERT: K 3 LYS cc_start: 0.8100 (tmtp) cc_final: 0.7586 (tptm) REVERT: K 5 TYR cc_start: 0.7860 (p90) cc_final: 0.7517 (p90) REVERT: N 16 GLN cc_start: 0.7696 (mt0) cc_final: 0.7376 (mt0) REVERT: O 3 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7454 (tmtt) REVERT: O 45 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7048 (tm-30) REVERT: P 25 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8669 (mpp) REVERT: Q 6 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8197 (tppp) REVERT: Q 41 TYR cc_start: 0.8124 (m-80) cc_final: 0.7914 (m-80) REVERT: Q 45 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7679 (tm-30) REVERT: S 3 LYS cc_start: 0.9108 (mttt) cc_final: 0.8661 (mmtm) REVERT: U 15 ARG cc_start: 0.8093 (mmt90) cc_final: 0.7069 (mtm110) REVERT: W 6 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8476 (mtmm) REVERT: W 9 MET cc_start: 0.8676 (mtp) cc_final: 0.8371 (mmt) REVERT: 1 26 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8342 (mp) REVERT: 1 45 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8077 (tp30) REVERT: 2 15 GLU cc_start: 0.6957 (pm20) cc_final: 0.6672 (pm20) REVERT: 2 25 MET cc_start: 0.7723 (mmm) cc_final: 0.7491 (mmm) REVERT: 9 10 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8636 (mt) REVERT: 0 19 GLU cc_start: 0.8576 (tt0) cc_final: 0.8339 (tm-30) REVERT: X 17 THR cc_start: 0.6810 (m) cc_final: 0.6108 (t) REVERT: X 28 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.5927 (tpt) REVERT: X 53 ARG cc_start: 0.6405 (mtt-85) cc_final: 0.5234 (ptm160) REVERT: X 55 LEU cc_start: 0.8558 (mt) cc_final: 0.8234 (mt) REVERT: Y 6 GLU cc_start: 0.7339 (tp30) cc_final: 0.6964 (tp30) REVERT: Y 10 ARG cc_start: 0.7536 (tpt90) cc_final: 0.7242 (mtt-85) REVERT: m 17 ASP cc_start: 0.8037 (t0) cc_final: 0.7580 (m-30) REVERT: m 21 THR cc_start: 0.8839 (m) cc_final: 0.8319 (t) REVERT: m 23 ASP cc_start: 0.7449 (t0) cc_final: 0.6773 (t0) REVERT: m 36 SER cc_start: 0.8767 (t) cc_final: 0.8498 (p) REVERT: m 122 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8545 (ttt) REVERT: h 173 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7593 (mp0) REVERT: h 231 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8125 (t0) REVERT: d 3 LYS cc_start: 0.8795 (mttt) cc_final: 0.8560 (mtpt) REVERT: d 5 TYR cc_start: 0.8835 (p90) cc_final: 0.8535 (p90) REVERT: e 18 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: f 9 MET cc_start: 0.7753 (mmm) cc_final: 0.7416 (mmp) REVERT: f 10 ILE cc_start: 0.7753 (mm) cc_final: 0.7469 (mt) REVERT: f 15 ARG cc_start: 0.7226 (mmt90) cc_final: 0.6375 (mtp-110) REVERT: g 12 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7635 (mp) REVERT: g 19 GLU cc_start: 0.8082 (tt0) cc_final: 0.7878 (tt0) REVERT: i 3 LYS cc_start: 0.8568 (mtpm) cc_final: 0.8071 (tppp) REVERT: i 5 TYR cc_start: 0.8050 (p90) cc_final: 0.7543 (p90) REVERT: k 3 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7849 (tmtp) REVERT: o 3 LYS cc_start: 0.8237 (ttmm) cc_final: 0.7620 (mtpp) REVERT: o 6 LYS cc_start: 0.7655 (mtpt) cc_final: 0.7366 (mmmt) REVERT: q 45 GLU cc_start: 0.8216 (tp30) cc_final: 0.7604 (tm-30) REVERT: q 53 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.5316 (mtt-85) REVERT: s 14 ARG cc_start: 0.8362 (mtm110) cc_final: 0.7837 (mtt90) REVERT: t 19 GLU cc_start: 0.7819 (pt0) cc_final: 0.7587 (pt0) REVERT: u 15 ARG cc_start: 0.8046 (mmt90) cc_final: 0.7600 (mtt90) REVERT: w 37 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8405 (p) REVERT: c 9 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7407 (m-10) REVERT: 5 5 TYR cc_start: 0.7963 (p90) cc_final: 0.7329 (p90) REVERT: b1 37 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8426 (p) REVERT: 4 15 GLU cc_start: 0.7968 (pt0) cc_final: 0.7626 (pm20) REVERT: 4 16 GLN cc_start: 0.7566 (mt0) cc_final: 0.7215 (mp-120) REVERT: b8 15 GLU cc_start: 0.7846 (mp0) cc_final: 0.7635 (pm20) REVERT: b9 10 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8614 (mt) REVERT: x 28 MET cc_start: 0.7680 (mtm) cc_final: 0.7037 (tmt) REVERT: x 53 ARG cc_start: 0.6398 (mtt-85) cc_final: 0.5262 (ptm160) REVERT: x 54 MET cc_start: 0.7191 (mtp) cc_final: 0.6713 (mtp) REVERT: y 6 GLU cc_start: 0.7408 (tp30) cc_final: 0.6872 (tp30) REVERT: y 36 LEU cc_start: 0.8459 (tp) cc_final: 0.8198 (tm) outliers start: 140 outliers final: 53 residues processed: 1010 average time/residue: 0.3584 time to fit residues: 471.8329 Evaluate side-chains 976 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 902 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 0 residue 14 ASP Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain m residue 122 MET Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain k residue 7 ILE Chi-restraints excluded: chain o residue 20 GLN Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 53 ARG Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 119 optimal weight: 6.9990 chunk 201 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 262 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 236 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 434 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 16 GLN Y 51 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 42 ASN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113537 restraints weight = 64421.767| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.91 r_work: 0.3169 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 46764 Z= 0.151 Angle : 0.644 12.111 64138 Z= 0.281 Chirality : 0.038 0.191 6216 Planarity : 0.003 0.030 7888 Dihedral : 15.866 179.969 8464 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.36 % Allowed : 22.14 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.12), residues: 4462 helix: 2.28 (0.09), residues: 2930 sheet: -0.71 (0.76), residues: 48 loop : 0.19 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 233 TYR 0.024 0.001 TYRb1 5 PHE 0.025 0.001 PHE 3 23 TRP 0.017 0.001 TRP Z 29 HIS 0.011 0.001 HIS 4 21 Details of bonding type rmsd covalent geometry : bond 0.00346 (46700) covalent geometry : angle 0.64357 (64138) hydrogen bonds : bond 0.04721 ( 2564) hydrogen bonds : angle 4.05189 ( 7407) Misc. bond : bond 0.00224 ( 64) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 933 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 201 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: L 257 ASP cc_start: 0.8520 (m-30) cc_final: 0.8222 (t70) REVERT: M 17 ASP cc_start: 0.8147 (t0) cc_final: 0.7603 (m-30) REVERT: M 21 THR cc_start: 0.8915 (m) cc_final: 0.8348 (t) REVERT: M 23 ASP cc_start: 0.7389 (t0) cc_final: 0.6778 (t0) REVERT: M 36 SER cc_start: 0.9010 (t) cc_final: 0.8658 (p) REVERT: M 60 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8208 (mp) REVERT: M 122 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8693 (ttt) REVERT: H 163 LYS cc_start: 0.8953 (pttt) cc_final: 0.8690 (ptmm) REVERT: H 184 LYS cc_start: 0.6946 (mmtp) cc_final: 0.6299 (ttmm) REVERT: H 226 THR cc_start: 0.8657 (p) cc_final: 0.8104 (t) REVERT: A 12 ASP cc_start: 0.8824 (t70) cc_final: 0.8553 (t0) REVERT: D 3 LYS cc_start: 0.8827 (mttt) cc_final: 0.8590 (mtpt) REVERT: D 5 TYR cc_start: 0.8874 (p90) cc_final: 0.8465 (p90) REVERT: E 26 SER cc_start: 0.9104 (m) cc_final: 0.8734 (p) REVERT: F 9 MET cc_start: 0.7828 (mmm) cc_final: 0.7548 (mmp) REVERT: F 10 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7547 (mt) REVERT: F 15 ARG cc_start: 0.7369 (mmt90) cc_final: 0.6468 (mtp-110) REVERT: G 12 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7653 (mp) REVERT: G 19 GLU cc_start: 0.8272 (tt0) cc_final: 0.8004 (tt0) REVERT: I 5 TYR cc_start: 0.8194 (p90) cc_final: 0.7953 (p90) REVERT: K 3 LYS cc_start: 0.8085 (tmtp) cc_final: 0.7815 (tmtp) REVERT: K 5 TYR cc_start: 0.7951 (p90) cc_final: 0.7659 (p90) REVERT: K 6 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7372 (tptp) REVERT: N 16 GLN cc_start: 0.7746 (mt0) cc_final: 0.7402 (mt0) REVERT: N 28 LEU cc_start: 0.8818 (tt) cc_final: 0.8612 (tp) REVERT: O 3 LYS cc_start: 0.8001 (ttmm) cc_final: 0.7429 (tmtt) REVERT: O 45 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7173 (tm-30) REVERT: Q 6 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8078 (tppp) REVERT: Q 45 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7746 (tm-30) REVERT: S 3 LYS cc_start: 0.9183 (mttt) cc_final: 0.8726 (mmtm) REVERT: S 14 ARG cc_start: 0.8351 (mtt90) cc_final: 0.8021 (mtt90) REVERT: T 19 GLU cc_start: 0.7826 (pt0) cc_final: 0.7583 (tm-30) REVERT: U 15 ARG cc_start: 0.8228 (mmt90) cc_final: 0.7144 (mtm110) REVERT: W 6 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8503 (mtmm) REVERT: W 9 MET cc_start: 0.8804 (mtp) cc_final: 0.8482 (mmt) REVERT: C 9 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: C 25 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8403 (mmm) REVERT: 1 45 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8112 (tp30) REVERT: 2 15 GLU cc_start: 0.6928 (pm20) cc_final: 0.6606 (pm20) REVERT: 9 10 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8692 (mt) REVERT: 0 19 GLU cc_start: 0.8842 (tt0) cc_final: 0.8590 (tm-30) REVERT: X 17 THR cc_start: 0.6767 (m) cc_final: 0.6075 (t) REVERT: X 28 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6159 (tpt) REVERT: X 53 ARG cc_start: 0.6406 (mtt-85) cc_final: 0.5208 (ptm160) REVERT: X 55 LEU cc_start: 0.8542 (mt) cc_final: 0.8218 (mt) REVERT: Y 6 GLU cc_start: 0.7449 (tp30) cc_final: 0.7093 (tp30) REVERT: Y 10 ARG cc_start: 0.7651 (tpt90) cc_final: 0.7372 (mtt-85) REVERT: m 17 ASP cc_start: 0.8225 (t0) cc_final: 0.7606 (m-30) REVERT: m 21 THR cc_start: 0.8919 (m) cc_final: 0.8428 (t) REVERT: m 23 ASP cc_start: 0.7490 (t0) cc_final: 0.6775 (t0) REVERT: m 122 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8689 (ttt) REVERT: h 173 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7753 (mp0) REVERT: d 3 LYS cc_start: 0.8855 (mttt) cc_final: 0.8594 (mtpt) REVERT: d 5 TYR cc_start: 0.8893 (p90) cc_final: 0.8585 (p90) REVERT: e 18 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8066 (mt0) REVERT: e 26 SER cc_start: 0.9103 (m) cc_final: 0.8734 (p) REVERT: f 9 MET cc_start: 0.7818 (mmm) cc_final: 0.7495 (mmp) REVERT: f 15 ARG cc_start: 0.7380 (mmt90) cc_final: 0.6459 (mtp-110) REVERT: g 12 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7696 (mp) REVERT: g 19 GLU cc_start: 0.8204 (tt0) cc_final: 0.7983 (tt0) REVERT: i 3 LYS cc_start: 0.8532 (mtpm) cc_final: 0.8058 (tppp) REVERT: i 5 TYR cc_start: 0.8041 (p90) cc_final: 0.7555 (p90) REVERT: k 3 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7863 (tmtp) REVERT: k 16 VAL cc_start: 0.9005 (t) cc_final: 0.8776 (p) REVERT: o 3 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7532 (mtpp) REVERT: o 6 LYS cc_start: 0.7737 (mtpt) cc_final: 0.7389 (mmmt) REVERT: o 45 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7559 (tm-30) REVERT: q 20 GLN cc_start: 0.8388 (tp40) cc_final: 0.7884 (tm-30) REVERT: q 45 GLU cc_start: 0.8331 (tp30) cc_final: 0.7691 (tm-30) REVERT: q 53 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.5332 (mtt-85) REVERT: s 14 ARG cc_start: 0.8409 (mtm110) cc_final: 0.7889 (mtt90) REVERT: u 15 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7745 (mtt90) REVERT: c 9 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7544 (m-10) REVERT: 5 5 TYR cc_start: 0.7981 (p90) cc_final: 0.7305 (p90) REVERT: b1 4 PHE cc_start: 0.6457 (OUTLIER) cc_final: 0.5748 (m-10) REVERT: b1 5 TYR cc_start: 0.7099 (p90) cc_final: 0.5960 (p90) REVERT: b1 37 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8467 (p) REVERT: 4 15 GLU cc_start: 0.7945 (pt0) cc_final: 0.7598 (pm20) REVERT: 4 16 GLN cc_start: 0.7622 (mt0) cc_final: 0.7257 (mp-120) REVERT: b9 10 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8675 (mt) REVERT: x 28 MET cc_start: 0.7784 (mtm) cc_final: 0.7083 (tmm) REVERT: x 53 ARG cc_start: 0.6359 (mtt-85) cc_final: 0.5187 (ptm160) REVERT: x 54 MET cc_start: 0.7253 (mtp) cc_final: 0.6770 (mtp) REVERT: y 6 GLU cc_start: 0.7549 (tp30) cc_final: 0.7002 (tp30) REVERT: y 36 LEU cc_start: 0.8473 (tp) cc_final: 0.8227 (tm) outliers start: 128 outliers final: 52 residues processed: 995 average time/residue: 0.3559 time to fit residues: 461.6902 Evaluate side-chains 976 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 903 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain C residue 9 TYR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 9 residue 30 MET Chi-restraints excluded: chain 0 residue 14 ASP Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain m residue 122 MET Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain k residue 7 ILE Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain k residue 46 ILE Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 53 ARG Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 31 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 193 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 373 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN 7 20 GLN 0 16 GLN X 26 GLN Y 51 ASN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 42 ASN o 20 GLN b1 20 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110199 restraints weight = 65052.987| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.93 r_work: 0.3113 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 46764 Z= 0.247 Angle : 0.743 11.555 64138 Z= 0.321 Chirality : 0.042 0.228 6216 Planarity : 0.004 0.048 7888 Dihedral : 16.234 179.944 8464 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.28 % Allowed : 22.85 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.12), residues: 4462 helix: 2.05 (0.09), residues: 2920 sheet: -0.95 (0.75), residues: 48 loop : 0.17 (0.17), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 233 TYR 0.027 0.002 TYR w 41 PHE 0.034 0.002 PHE k 23 TRP 0.020 0.002 TRP Z 29 HIS 0.013 0.002 HIS z 21 Details of bonding type rmsd covalent geometry : bond 0.00588 (46700) covalent geometry : angle 0.74322 (64138) hydrogen bonds : bond 0.05025 ( 2564) hydrogen bonds : angle 4.21270 ( 7407) Misc. bond : bond 0.00370 ( 64) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 910 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 257 ASP cc_start: 0.8433 (m-30) cc_final: 0.8192 (t0) REVERT: M 17 ASP cc_start: 0.8200 (t0) cc_final: 0.7674 (m-30) REVERT: M 21 THR cc_start: 0.8944 (m) cc_final: 0.8400 (t) REVERT: M 23 ASP cc_start: 0.7459 (t0) cc_final: 0.6837 (t0) REVERT: M 110 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8380 (mtpm) REVERT: H 163 LYS cc_start: 0.8979 (pttt) cc_final: 0.8742 (ptmm) REVERT: H 184 LYS cc_start: 0.7029 (mmtp) cc_final: 0.6413 (ttmm) REVERT: H 226 THR cc_start: 0.8732 (p) cc_final: 0.8179 (t) REVERT: A 12 ASP cc_start: 0.8854 (t70) cc_final: 0.8611 (t0) REVERT: D 3 LYS cc_start: 0.8853 (mttt) cc_final: 0.8638 (mtpt) REVERT: D 5 TYR cc_start: 0.8944 (p90) cc_final: 0.8715 (p90) REVERT: F 9 MET cc_start: 0.7928 (mmm) cc_final: 0.7667 (mmp) REVERT: F 15 ARG cc_start: 0.7557 (mmt90) cc_final: 0.6584 (mtp-110) REVERT: G 12 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7681 (mp) REVERT: G 19 GLU cc_start: 0.8199 (tt0) cc_final: 0.7915 (tt0) REVERT: I 3 LYS cc_start: 0.8423 (mtpm) cc_final: 0.8026 (tppp) REVERT: I 5 TYR cc_start: 0.8214 (p90) cc_final: 0.7993 (p90) REVERT: K 3 LYS cc_start: 0.8181 (tmtp) cc_final: 0.7948 (tmtp) REVERT: K 5 TYR cc_start: 0.8009 (p90) cc_final: 0.7771 (p90) REVERT: K 15 ARG cc_start: 0.7043 (mmt180) cc_final: 0.6156 (mtm110) REVERT: K 27 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8328 (tt) REVERT: K 38 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.7937 (p) REVERT: N 16 GLN cc_start: 0.7684 (mt0) cc_final: 0.7315 (mt0) REVERT: N 28 LEU cc_start: 0.8881 (tt) cc_final: 0.8681 (tp) REVERT: O 3 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7517 (tmtt) REVERT: O 45 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7300 (tm-30) REVERT: Q 6 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8197 (tppp) REVERT: Q 45 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7769 (tm-30) REVERT: S 3 LYS cc_start: 0.9231 (mttt) cc_final: 0.8796 (mmtm) REVERT: U 15 ARG cc_start: 0.8269 (mmt90) cc_final: 0.7261 (mtm110) REVERT: W 6 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8647 (mtmm) REVERT: W 9 MET cc_start: 0.8926 (mtp) cc_final: 0.8681 (mmt) REVERT: W 11 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8795 (m-10) REVERT: 1 45 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8158 (tp30) REVERT: 2 15 GLU cc_start: 0.7015 (pm20) cc_final: 0.6701 (pm20) REVERT: 9 10 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8748 (mt) REVERT: 0 19 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: X 17 THR cc_start: 0.6947 (m) cc_final: 0.6226 (t) REVERT: X 28 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6786 (tmm) REVERT: X 53 ARG cc_start: 0.6405 (mtt-85) cc_final: 0.5165 (ptm160) REVERT: X 55 LEU cc_start: 0.8695 (mt) cc_final: 0.8367 (mt) REVERT: Y 6 GLU cc_start: 0.7422 (tp30) cc_final: 0.6485 (pm20) REVERT: m 17 ASP cc_start: 0.8125 (t0) cc_final: 0.7562 (m-30) REVERT: m 21 THR cc_start: 0.9051 (m) cc_final: 0.8600 (t) REVERT: m 23 ASP cc_start: 0.7541 (t0) cc_final: 0.6850 (t0) REVERT: h 173 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7747 (mp0) REVERT: d 3 LYS cc_start: 0.8884 (mttt) cc_final: 0.8637 (mtpt) REVERT: d 5 TYR cc_start: 0.8935 (p90) cc_final: 0.8585 (p90) REVERT: e 18 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: f 3 LYS cc_start: 0.8547 (tppp) cc_final: 0.8337 (ttmm) REVERT: f 9 MET cc_start: 0.7999 (mmm) cc_final: 0.7621 (mmp) REVERT: f 15 ARG cc_start: 0.7525 (mmt90) cc_final: 0.6552 (mtp-110) REVERT: g 12 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7703 (mp) REVERT: g 19 GLU cc_start: 0.8184 (tt0) cc_final: 0.7978 (tt0) REVERT: i 3 LYS cc_start: 0.8565 (mtpm) cc_final: 0.8090 (tppp) REVERT: i 5 TYR cc_start: 0.8045 (p90) cc_final: 0.7534 (p90) REVERT: n 28 LEU cc_start: 0.8812 (tt) cc_final: 0.8539 (tp) REVERT: o 3 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7624 (mtpp) REVERT: o 6 LYS cc_start: 0.7547 (mtpt) cc_final: 0.7170 (mmmt) REVERT: o 45 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7626 (tm-30) REVERT: q 9 MET cc_start: 0.8315 (mtm) cc_final: 0.8079 (mtm) REVERT: q 20 GLN cc_start: 0.8416 (tp40) cc_final: 0.8037 (tm-30) REVERT: q 45 GLU cc_start: 0.8357 (tp30) cc_final: 0.7712 (tm-30) REVERT: q 53 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.5660 (mtt-85) REVERT: s 14 ARG cc_start: 0.8548 (mtm110) cc_final: 0.8326 (mtt90) REVERT: u 15 ARG cc_start: 0.8241 (mmt90) cc_final: 0.7780 (mtt90) REVERT: 5 5 TYR cc_start: 0.8071 (p90) cc_final: 0.7473 (p90) REVERT: b1 4 PHE cc_start: 0.6513 (OUTLIER) cc_final: 0.5999 (m-10) REVERT: b1 5 TYR cc_start: 0.7137 (p90) cc_final: 0.5820 (p90) REVERT: b1 37 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8460 (p) REVERT: 4 15 GLU cc_start: 0.7944 (pt0) cc_final: 0.7593 (pm20) REVERT: 4 16 GLN cc_start: 0.7636 (mt0) cc_final: 0.7253 (mp-120) REVERT: b9 10 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8724 (mt) REVERT: x 28 MET cc_start: 0.7750 (mtm) cc_final: 0.7122 (tmt) REVERT: x 47 PHE cc_start: 0.7772 (t80) cc_final: 0.7427 (t80) REVERT: x 53 ARG cc_start: 0.6460 (mtt-85) cc_final: 0.5265 (ptm160) REVERT: x 54 MET cc_start: 0.7282 (mtp) cc_final: 0.7011 (mtp) REVERT: y 6 GLU cc_start: 0.7558 (tp30) cc_final: 0.7005 (tp30) REVERT: y 36 LEU cc_start: 0.8439 (tp) cc_final: 0.8218 (tm) outliers start: 125 outliers final: 60 residues processed: 969 average time/residue: 0.3600 time to fit residues: 453.7135 Evaluate side-chains 965 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 889 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 0 residue 14 ASP Chi-restraints excluded: chain 0 residue 16 GLN Chi-restraints excluded: chain 0 residue 19 GLU Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain k residue 7 ILE Chi-restraints excluded: chain o residue 20 GLN Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 53 ARG Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain t residue 40 LEU Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 29 TRP Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 260 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 292 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 274 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 422 optimal weight: 0.9990 chunk 355 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN Q 20 GLN 7 20 GLN ** 0 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112985 restraints weight = 64499.188| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.95 r_work: 0.3167 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 46764 Z= 0.155 Angle : 0.677 12.612 64138 Z= 0.299 Chirality : 0.039 0.201 6216 Planarity : 0.003 0.067 7888 Dihedral : 15.933 179.989 8464 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.55 % Allowed : 23.90 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.12), residues: 4462 helix: 2.18 (0.09), residues: 2920 sheet: -0.85 (0.76), residues: 48 loop : 0.15 (0.17), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 233 TYR 0.023 0.001 TYR m 76 PHE 0.032 0.001 PHE o 25 TRP 0.022 0.001 TRP 2 29 HIS 0.012 0.001 HIS z 21 Details of bonding type rmsd covalent geometry : bond 0.00357 (46700) covalent geometry : angle 0.67688 (64138) hydrogen bonds : bond 0.04798 ( 2564) hydrogen bonds : angle 4.13511 ( 7407) Misc. bond : bond 0.00220 ( 64) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 931 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 257 ASP cc_start: 0.8395 (m-30) cc_final: 0.8129 (t0) REVERT: M 17 ASP cc_start: 0.8147 (t0) cc_final: 0.7604 (m-30) REVERT: M 21 THR cc_start: 0.8903 (m) cc_final: 0.8334 (t) REVERT: M 23 ASP cc_start: 0.7372 (t0) cc_final: 0.6762 (t0) REVERT: M 110 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8363 (mtpm) REVERT: H 163 LYS cc_start: 0.8953 (pttt) cc_final: 0.8684 (ptmm) REVERT: H 184 LYS cc_start: 0.7142 (mmtp) cc_final: 0.6475 (ttmm) REVERT: H 226 THR cc_start: 0.8654 (p) cc_final: 0.8083 (t) REVERT: A 12 ASP cc_start: 0.8825 (t70) cc_final: 0.8546 (t0) REVERT: D 3 LYS cc_start: 0.8852 (mttt) cc_final: 0.8603 (mtpt) REVERT: D 5 TYR cc_start: 0.8877 (p90) cc_final: 0.8480 (p90) REVERT: E 26 SER cc_start: 0.9109 (m) cc_final: 0.8749 (p) REVERT: F 9 MET cc_start: 0.7934 (mmm) cc_final: 0.7635 (mmp) REVERT: F 15 ARG cc_start: 0.7399 (mmt90) cc_final: 0.6475 (mtp-110) REVERT: G 12 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7591 (mp) REVERT: G 19 GLU cc_start: 0.8248 (tt0) cc_final: 0.7977 (tt0) REVERT: I 3 LYS cc_start: 0.8416 (mtpm) cc_final: 0.8018 (tppp) REVERT: I 5 TYR cc_start: 0.8201 (p90) cc_final: 0.7976 (p90) REVERT: K 3 LYS cc_start: 0.8138 (tmtp) cc_final: 0.7868 (tmtp) REVERT: K 5 TYR cc_start: 0.7977 (p90) cc_final: 0.7764 (p90) REVERT: K 15 ARG cc_start: 0.7001 (mmt180) cc_final: 0.6138 (mtm110) REVERT: K 27 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8244 (tt) REVERT: N 16 GLN cc_start: 0.7660 (mt0) cc_final: 0.7314 (mt0) REVERT: O 3 LYS cc_start: 0.8017 (ttmm) cc_final: 0.7475 (tmtt) REVERT: O 5 TYR cc_start: 0.7959 (p90) cc_final: 0.7538 (p90) REVERT: O 45 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7220 (tm-30) REVERT: Q 45 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7759 (tm-30) REVERT: S 3 LYS cc_start: 0.9223 (mttt) cc_final: 0.8774 (mmtm) REVERT: S 14 ARG cc_start: 0.8406 (mtt90) cc_final: 0.8107 (mtt90) REVERT: T 19 GLU cc_start: 0.7705 (pt0) cc_final: 0.7501 (tm-30) REVERT: U 15 ARG cc_start: 0.8170 (mmt90) cc_final: 0.7080 (mtm110) REVERT: W 6 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8583 (mtmm) REVERT: C 25 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8424 (mmm) REVERT: 1 4 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.5366 (m-10) REVERT: 1 6 LYS cc_start: 0.7432 (mmtp) cc_final: 0.7116 (mmtm) REVERT: 1 45 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8166 (tp30) REVERT: 2 15 GLU cc_start: 0.7006 (pm20) cc_final: 0.6716 (pt0) REVERT: 2 43 TYR cc_start: 0.7699 (t80) cc_final: 0.7318 (t80) REVERT: 9 10 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8697 (mt) REVERT: 0 19 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8552 (tm-30) REVERT: X 17 THR cc_start: 0.6891 (m) cc_final: 0.6217 (t) REVERT: X 28 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6178 (tpt) REVERT: X 53 ARG cc_start: 0.6394 (mtt-85) cc_final: 0.5188 (ptm160) REVERT: X 55 LEU cc_start: 0.8561 (mt) cc_final: 0.8226 (mt) REVERT: Y 6 GLU cc_start: 0.7539 (tp30) cc_final: 0.6567 (pm20) REVERT: Y 10 ARG cc_start: 0.7746 (tpt90) cc_final: 0.7151 (ttt90) REVERT: m 17 ASP cc_start: 0.8180 (t0) cc_final: 0.7587 (m-30) REVERT: m 21 THR cc_start: 0.8929 (m) cc_final: 0.8486 (t) REVERT: m 23 ASP cc_start: 0.7467 (t0) cc_final: 0.6763 (t0) REVERT: h 173 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7701 (mp0) REVERT: h 193 MET cc_start: 0.8282 (mmt) cc_final: 0.8052 (tpt) REVERT: d 3 LYS cc_start: 0.8872 (mttt) cc_final: 0.8617 (mtpt) REVERT: d 5 TYR cc_start: 0.8882 (p90) cc_final: 0.8621 (p90) REVERT: e 26 SER cc_start: 0.9105 (m) cc_final: 0.8746 (p) REVERT: f 3 LYS cc_start: 0.8535 (tppp) cc_final: 0.8330 (ttmt) REVERT: f 15 ARG cc_start: 0.7472 (mmt90) cc_final: 0.6481 (mtp-110) REVERT: g 19 GLU cc_start: 0.8135 (tt0) cc_final: 0.7905 (tt0) REVERT: i 3 LYS cc_start: 0.8573 (mtpm) cc_final: 0.8073 (tppp) REVERT: i 5 TYR cc_start: 0.8085 (p90) cc_final: 0.7577 (p90) REVERT: k 3 LYS cc_start: 0.8325 (tmtp) cc_final: 0.7939 (tptm) REVERT: o 3 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7573 (mtpp) REVERT: o 6 LYS cc_start: 0.7684 (mtpt) cc_final: 0.7305 (mmmt) REVERT: o 45 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7560 (tm-30) REVERT: q 20 GLN cc_start: 0.8410 (tp40) cc_final: 0.8015 (tm-30) REVERT: q 45 GLU cc_start: 0.8326 (tp30) cc_final: 0.7701 (tm-30) REVERT: q 53 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.5360 (mtt-85) REVERT: s 14 ARG cc_start: 0.8518 (mtm110) cc_final: 0.8303 (mtt90) REVERT: u 15 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7755 (mtt90) REVERT: c 9 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: 5 5 TYR cc_start: 0.8006 (p90) cc_final: 0.7467 (p90) REVERT: b1 3 LYS cc_start: 0.5776 (mttm) cc_final: 0.5128 (mttm) REVERT: b1 4 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.6039 (m-10) REVERT: b1 5 TYR cc_start: 0.7180 (p90) cc_final: 0.5740 (p90) REVERT: b1 37 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8414 (p) REVERT: 4 15 GLU cc_start: 0.7931 (pt0) cc_final: 0.7677 (pm20) REVERT: 4 16 GLN cc_start: 0.7615 (mt0) cc_final: 0.7261 (mp-120) REVERT: b9 10 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8680 (mt) REVERT: x 28 MET cc_start: 0.7766 (mtm) cc_final: 0.7080 (tmt) REVERT: x 47 PHE cc_start: 0.7790 (t80) cc_final: 0.7460 (t80) REVERT: x 53 ARG cc_start: 0.6411 (mtt-85) cc_final: 0.5229 (ptm160) REVERT: x 54 MET cc_start: 0.7209 (mtp) cc_final: 0.6721 (mtp) REVERT: y 6 GLU cc_start: 0.7568 (tp30) cc_final: 0.7024 (tp30) REVERT: y 36 LEU cc_start: 0.8436 (tp) cc_final: 0.8204 (tm) outliers start: 97 outliers final: 58 residues processed: 983 average time/residue: 0.3459 time to fit residues: 444.4022 Evaluate side-chains 974 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 902 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 0 residue 19 GLU Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain k residue 7 ILE Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 53 ARG Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain t residue 40 LEU Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 262 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 200 optimal weight: 0.0980 chunk 330 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 293 optimal weight: 0.0670 chunk 207 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 431 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 77 GLN ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN Q 20 GLN ** 2 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 16 GLN Y 51 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 16 GLN b1 20 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116096 restraints weight = 64840.145| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.13 r_work: 0.3201 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 46764 Z= 0.125 Angle : 0.647 12.599 64138 Z= 0.289 Chirality : 0.039 0.261 6216 Planarity : 0.003 0.055 7888 Dihedral : 15.520 179.995 8464 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.97 % Allowed : 24.92 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.12), residues: 4462 helix: 2.29 (0.09), residues: 2934 sheet: -0.63 (0.78), residues: 48 loop : 0.20 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 233 TYR 0.028 0.001 TYR U 5 PHE 0.046 0.001 PHE K 23 TRP 0.035 0.001 TRP j 29 HIS 0.010 0.001 HIS z 21 Details of bonding type rmsd covalent geometry : bond 0.00275 (46700) covalent geometry : angle 0.64663 (64138) hydrogen bonds : bond 0.04610 ( 2564) hydrogen bonds : angle 4.06142 ( 7407) Misc. bond : bond 0.00128 ( 64) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 975 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 257 ASP cc_start: 0.8221 (m-30) cc_final: 0.8012 (t0) REVERT: M 17 ASP cc_start: 0.7964 (t0) cc_final: 0.7611 (m-30) REVERT: M 21 THR cc_start: 0.8701 (m) cc_final: 0.8144 (t) REVERT: M 23 ASP cc_start: 0.7217 (t0) cc_final: 0.6636 (t0) REVERT: H 163 LYS cc_start: 0.8843 (pttt) cc_final: 0.8590 (ptmm) REVERT: H 226 THR cc_start: 0.8564 (p) cc_final: 0.7970 (t) REVERT: A 22 VAL cc_start: 0.9226 (t) cc_final: 0.9023 (t) REVERT: D 3 LYS cc_start: 0.8815 (mttt) cc_final: 0.8614 (mtpt) REVERT: D 5 TYR cc_start: 0.8722 (p90) cc_final: 0.8364 (p90) REVERT: E 24 TYR cc_start: 0.8781 (t80) cc_final: 0.8541 (t80) REVERT: E 26 SER cc_start: 0.8949 (m) cc_final: 0.8663 (p) REVERT: F 9 MET cc_start: 0.7603 (mmm) cc_final: 0.7286 (mmp) REVERT: F 15 ARG cc_start: 0.7285 (mmt90) cc_final: 0.6385 (mtp-110) REVERT: G 12 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7348 (mp) REVERT: G 19 GLU cc_start: 0.8141 (tt0) cc_final: 0.7876 (tt0) REVERT: I 3 LYS cc_start: 0.8392 (mtpm) cc_final: 0.8008 (tppp) REVERT: K 3 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7602 (tptm) REVERT: K 20 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8301 (pm20) REVERT: N 16 GLN cc_start: 0.7744 (mt0) cc_final: 0.7287 (mt0) REVERT: N 25 MET cc_start: 0.8257 (mmm) cc_final: 0.7957 (mmm) REVERT: O 3 LYS cc_start: 0.7942 (ttmm) cc_final: 0.7386 (tmtt) REVERT: O 5 TYR cc_start: 0.7850 (p90) cc_final: 0.7116 (p90) REVERT: O 11 PHE cc_start: 0.6968 (m-80) cc_final: 0.6725 (m-80) REVERT: O 45 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6994 (tm-30) REVERT: P 20 LEU cc_start: 0.8585 (mt) cc_final: 0.8281 (tp) REVERT: Q 6 LYS cc_start: 0.8322 (tppt) cc_final: 0.7887 (tppp) REVERT: S 3 LYS cc_start: 0.9195 (mttt) cc_final: 0.8760 (mmtm) REVERT: S 14 ARG cc_start: 0.8350 (mtt90) cc_final: 0.8039 (mtt90) REVERT: U 5 TYR cc_start: 0.8848 (p90) cc_final: 0.8634 (p90) REVERT: U 15 ARG cc_start: 0.8039 (mmt90) cc_final: 0.7705 (mtt90) REVERT: W 6 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8503 (mtmm) REVERT: C 25 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8345 (mmm) REVERT: 1 4 PHE cc_start: 0.5985 (OUTLIER) cc_final: 0.5447 (m-10) REVERT: 1 5 TYR cc_start: 0.6835 (p90) cc_final: 0.5604 (p90) REVERT: 1 6 LYS cc_start: 0.7365 (mmtp) cc_final: 0.6999 (mmtt) REVERT: 1 45 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8111 (tp30) REVERT: 1 50 LYS cc_start: 0.7904 (ttmm) cc_final: 0.7533 (tttt) REVERT: 2 15 GLU cc_start: 0.7220 (pm20) cc_final: 0.6989 (pt0) REVERT: 2 43 TYR cc_start: 0.7619 (t80) cc_final: 0.7309 (t80) REVERT: 7 1 MET cc_start: 0.6005 (ptm) cc_final: 0.5534 (ttm) REVERT: 9 3 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8822 (mmmt) REVERT: 9 10 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8588 (mt) REVERT: X 17 THR cc_start: 0.6697 (m) cc_final: 0.6051 (t) REVERT: X 28 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.5899 (tpt) REVERT: X 53 ARG cc_start: 0.6353 (mtt-85) cc_final: 0.5277 (ptm160) REVERT: Y 6 GLU cc_start: 0.7495 (tp30) cc_final: 0.7052 (tp30) REVERT: Y 10 ARG cc_start: 0.7587 (tpt90) cc_final: 0.7251 (tpt90) REVERT: m 17 ASP cc_start: 0.8026 (t0) cc_final: 0.7620 (m-30) REVERT: m 21 THR cc_start: 0.8756 (m) cc_final: 0.8309 (t) REVERT: m 23 ASP cc_start: 0.7403 (t0) cc_final: 0.6840 (t0) REVERT: h 173 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7623 (mp0) REVERT: a 38 THR cc_start: 0.6907 (OUTLIER) cc_final: 0.6425 (p) REVERT: d 5 TYR cc_start: 0.8730 (p90) cc_final: 0.8408 (p90) REVERT: e 24 TYR cc_start: 0.8784 (t80) cc_final: 0.8558 (t80) REVERT: e 26 SER cc_start: 0.8935 (m) cc_final: 0.8642 (p) REVERT: f 9 MET cc_start: 0.7689 (mmm) cc_final: 0.7409 (mmp) REVERT: f 15 ARG cc_start: 0.7273 (mmt90) cc_final: 0.6353 (mtp-110) REVERT: g 12 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7195 (mp) REVERT: g 19 GLU cc_start: 0.7999 (tt0) cc_final: 0.7770 (tt0) REVERT: i 3 LYS cc_start: 0.8649 (mtpm) cc_final: 0.8153 (tppp) REVERT: i 5 TYR cc_start: 0.8068 (p90) cc_final: 0.7568 (p90) REVERT: k 3 LYS cc_start: 0.8166 (tmtp) cc_final: 0.7666 (tptm) REVERT: o 3 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7523 (mtpp) REVERT: p 20 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8319 (tp) REVERT: q 6 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7962 (mmtp) REVERT: q 20 GLN cc_start: 0.8343 (tp40) cc_final: 0.7956 (tm-30) REVERT: q 45 GLU cc_start: 0.8104 (tp30) cc_final: 0.7576 (tm-30) REVERT: q 53 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.4995 (mtt-85) REVERT: s 14 ARG cc_start: 0.8478 (mtm110) cc_final: 0.8250 (mtm-85) REVERT: t 14 ASP cc_start: 0.7854 (t0) cc_final: 0.7351 (p0) REVERT: u 15 ARG cc_start: 0.8011 (mmt90) cc_final: 0.7586 (mtt90) REVERT: 5 5 TYR cc_start: 0.7948 (p90) cc_final: 0.7457 (p90) REVERT: 5 9 MET cc_start: 0.8175 (mpp) cc_final: 0.7919 (mpt) REVERT: b1 4 PHE cc_start: 0.6363 (OUTLIER) cc_final: 0.6025 (m-10) REVERT: b1 5 TYR cc_start: 0.7137 (p90) cc_final: 0.5746 (p90) REVERT: b1 37 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8547 (p) REVERT: 6 1 MET cc_start: 0.6049 (ptm) cc_final: 0.5554 (ttm) REVERT: b9 10 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8581 (mt) REVERT: x 28 MET cc_start: 0.7725 (mtm) cc_final: 0.6706 (tpt) REVERT: x 47 PHE cc_start: 0.7711 (t80) cc_final: 0.7464 (t80) REVERT: x 53 ARG cc_start: 0.6352 (mtt-85) cc_final: 0.5247 (ptm160) REVERT: y 6 GLU cc_start: 0.7472 (tp30) cc_final: 0.6888 (tp30) REVERT: y 10 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7281 (mtt-85) REVERT: y 36 LEU cc_start: 0.8490 (tp) cc_final: 0.8223 (tm) outliers start: 75 outliers final: 31 residues processed: 1015 average time/residue: 0.3506 time to fit residues: 466.0900 Evaluate side-chains 954 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 907 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 10 ILE Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain l residue 46 ILE Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain k residue 7 ILE Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain p residue 20 LEU Chi-restraints excluded: chain q residue 53 ARG Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 10 ILE Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain y residue 10 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 211 optimal weight: 1.9990 chunk 368 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 360 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 347 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 243 optimal weight: 0.0470 chunk 153 optimal weight: 2.9990 chunk 432 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN D 20 GLN K 52 ASN P 16 GLN Q 20 GLN 0 16 GLN X 58 GLN Y 51 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 20 GLN i 20 GLN ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 16 GLN b1 20 GLN x 26 GLN x 58 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115228 restraints weight = 64772.335| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.91 r_work: 0.3202 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 46764 Z= 0.144 Angle : 0.672 13.083 64138 Z= 0.300 Chirality : 0.040 0.320 6216 Planarity : 0.003 0.053 7888 Dihedral : 15.476 179.972 8458 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.76 % Allowed : 26.10 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.12), residues: 4462 helix: 2.29 (0.09), residues: 2930 sheet: -0.64 (0.77), residues: 48 loop : 0.19 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 233 TYR 0.025 0.002 TYR N 24 PHE 0.030 0.001 PHE o 25 TRP 0.039 0.001 TRP j 29 HIS 0.010 0.001 HIS z 21 Details of bonding type rmsd covalent geometry : bond 0.00330 (46700) covalent geometry : angle 0.67248 (64138) hydrogen bonds : bond 0.04642 ( 2564) hydrogen bonds : angle 4.08345 ( 7407) Misc. bond : bond 0.00191 ( 64) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11883.47 seconds wall clock time: 202 minutes 45.86 seconds (12165.86 seconds total)