Starting phenix.real_space_refine on Wed Aug 27 03:13:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vor_32058/08_2025/7vor_32058.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vor_32058/08_2025/7vor_32058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vor_32058/08_2025/7vor_32058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vor_32058/08_2025/7vor_32058.map" model { file = "/net/cci-nas-00/data/ceres_data/7vor_32058/08_2025/7vor_32058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vor_32058/08_2025/7vor_32058.cif" } resolution = 2.74 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 24 5.49 5 Mg 64 5.21 5 S 174 5.16 5 C 31612 2.51 5 N 6300 2.21 5 O 6804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s 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: 44980 Number of models: 1 Model: "" Number of chains: 128 Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "H" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1973 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "A" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "J" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "R" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "V" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "W" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 437 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "Z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 392 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "2" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "7" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "0" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "X" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 529 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "Y" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 361 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "l" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "h" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1973 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "a" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "b" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "d" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "e" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "f" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "g" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "j" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "k" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "n" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "o" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "p" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "r" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "s" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "t" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "u" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "v" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "w" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "c" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "5" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 437 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "b1" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 392 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "4" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "b8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "b9" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "b0" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "x" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 529 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "y" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 361 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "L" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 354 Unusual residues: {'BCL': 2, 'BPH': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "M" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 360 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "A" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 222 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "E" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "2" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "7" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 122 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 354 Unusual residues: {'BCL': 2, 'BPH': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "m" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 360 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "h" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "a" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 222 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "b" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "e" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "g" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "r" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "t" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "v" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "b1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "6" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 122 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "b9" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "x" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.58, per 1000 atoms: 0.19 Number of scatterers: 44980 At special positions: 0 Unit cell: (225.68, 142.48, 107.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 174 16.00 P 24 15.00 Mg 64 11.99 O 6804 8.00 N 6300 7.00 C 31612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=64, symmetry=0 Number of additional bonds: simple=64, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8576 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 14 sheets defined 73.2% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'L' and resid 5 through 10 removed outlier: 3.921A pdb=" N LYS L 8 " --> pdb=" O PHE L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 57 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.571A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 Processing helix chain 'L' and resid 151 through 164 removed outlier: 3.981A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 169 removed outlier: 6.013A pdb=" N HIS L 168 " --> pdb=" O GLY L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 Processing helix chain 'L' and resid 225 through 251 Processing helix chain 'L' and resid 258 through 268 removed outlier: 3.537A pdb=" N TRP L 262 " --> pdb=" O GLN L 258 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 41 Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 140 removed outlier: 3.572A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 178 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 227 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 263 through 287 removed outlier: 3.753A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'H' and resid 12 through 36 Processing helix chain 'H' and resid 67 through 70 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.995A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 removed outlier: 3.840A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 259 Processing helix chain 'A' and resid 3 through 5 No H-bonds generated for 'chain 'A' and resid 3 through 5' Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'B' and resid 13 through 46 Processing helix chain 'D' and resid 1 through 5 removed outlier: 4.436A pdb=" N TYR D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 38 Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'E' and resid 13 through 46 Processing helix chain 'F' and resid 2 through 10 removed outlier: 4.425A pdb=" N TYR F 5 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'G' and resid 13 through 46 Processing helix chain 'I' and resid 3 through 10 Processing helix chain 'I' and resid 12 through 38 Processing helix chain 'I' and resid 42 through 51 Processing helix chain 'J' and resid 13 through 46 Processing helix chain 'K' and resid 3 through 10 Processing helix chain 'K' and resid 12 through 38 Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'N' and resid 13 through 46 Processing helix chain 'O' and resid 3 through 10 Processing helix chain 'O' and resid 12 through 38 Processing helix chain 'O' and resid 42 through 51 Processing helix chain 'P' and resid 13 through 46 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 51 Processing helix chain 'R' and resid 13 through 46 Processing helix chain 'S' and resid 3 through 10 Processing helix chain 'S' and resid 12 through 38 Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 13 through 46 Processing helix chain 'U' and resid 3 through 10 removed outlier: 3.562A pdb=" N LYS U 6 " --> pdb=" O LYS U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 12 through 38 Processing helix chain 'U' and resid 42 through 51 Processing helix chain 'V' and resid 13 through 46 Processing helix chain 'W' and resid 3 through 10 Processing helix chain 'W' and resid 12 through 38 Processing helix chain 'W' and resid 42 through 51 Processing helix chain 'C' and resid 13 through 46 Processing helix chain '3' and resid 4 through 10 removed outlier: 3.615A pdb=" N ILE 3 7 " --> pdb=" O PHE 3 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE 3 10 " --> pdb=" O ILE 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 38 removed outlier: 3.647A pdb=" N THR 3 38 " --> pdb=" O ILE 3 34 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 51 Processing helix chain 'Z' and resid 13 through 46 Processing helix chain '1' and resid 12 through 38 Processing helix chain '1' and resid 42 through 51 Processing helix chain '2' and resid 13 through 46 Processing helix chain '7' and resid 3 through 10 Processing helix chain '7' and resid 12 through 38 Processing helix chain '8' and resid 13 through 46 Processing helix chain '9' and resid 3 through 10 Processing helix chain '9' and resid 12 through 38 Processing helix chain '9' and resid 42 through 51 Processing helix chain '0' and resid 13 through 46 Processing helix chain 'X' and resid 9 through 13 Processing helix chain 'X' and resid 14 through 55 Processing helix chain 'Y' and resid 5 through 29 Processing helix chain 'Y' and resid 31 through 49 removed outlier: 4.250A pdb=" N GLY Y 35 " --> pdb=" O HIS Y 31 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR Y 49 " --> pdb=" O PHE Y 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 10 removed outlier: 3.920A pdb=" N LYS l 8 " --> pdb=" O PHE l 5 " (cutoff:3.500A) Processing helix chain 'l' and resid 31 through 57 Processing helix chain 'l' and resid 70 through 74 Processing helix chain 'l' and resid 79 through 82 Processing helix chain 'l' and resid 83 through 112 Processing helix chain 'l' and resid 115 through 133 removed outlier: 3.571A pdb=" N PHE l 123 " --> pdb=" O PHE l 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 133 through 140 Processing helix chain 'l' and resid 141 through 145 Processing helix chain 'l' and resid 151 through 164 removed outlier: 3.981A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 165 through 169 removed outlier: 6.012A pdb=" N HIS l 168 " --> pdb=" O GLY l 165 " (cutoff:3.500A) Processing helix chain 'l' and resid 170 through 199 Processing helix chain 'l' and resid 208 through 221 Processing helix chain 'l' and resid 225 through 251 Processing helix chain 'l' and resid 258 through 268 removed outlier: 3.537A pdb=" N TRP l 262 " --> pdb=" O GLN l 258 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP l 265 " --> pdb=" O ASP l 261 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP l 266 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 41 Processing helix chain 'm' and resid 53 through 78 Processing helix chain 'm' and resid 81 through 88 Processing helix chain 'm' and resid 98 through 102 Processing helix chain 'm' and resid 108 through 111 Processing helix chain 'm' and resid 112 through 140 removed outlier: 3.573A pdb=" N LEU m 140 " --> pdb=" O ARG m 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 144 through 162 Processing helix chain 'm' and resid 162 through 169 Processing helix chain 'm' and resid 170 through 174 Processing helix chain 'm' and resid 178 through 193 Processing helix chain 'm' and resid 195 through 198 Processing helix chain 'm' and resid 199 through 227 Processing helix chain 'm' and resid 228 through 230 No H-bonds generated for 'chain 'm' and resid 228 through 230' Processing helix chain 'm' and resid 233 through 240 Processing helix chain 'm' and resid 242 through 257 Processing helix chain 'm' and resid 263 through 287 removed outlier: 3.753A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 293 through 301 Processing helix chain 'h' and resid 12 through 36 Processing helix chain 'h' and resid 67 through 70 Processing helix chain 'h' and resid 103 through 108 Processing helix chain 'h' and resid 109 through 113 Processing helix chain 'h' and resid 194 through 196 No H-bonds generated for 'chain 'h' and resid 194 through 196' Processing helix chain 'h' and resid 209 through 216 removed outlier: 3.995A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) Processing helix chain 'h' and resid 226 through 244 removed outlier: 3.840A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 250 through 259 Processing helix chain 'a' and resid 3 through 5 No H-bonds generated for 'chain 'a' and resid 3 through 5' Processing helix chain 'a' and resid 6 through 11 Processing helix chain 'a' and resid 12 through 38 Processing helix chain 'a' and resid 42 through 51 Processing helix chain 'b' and resid 13 through 46 Processing helix chain 'd' and resid 1 through 5 removed outlier: 4.436A pdb=" N TYR d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 11 Processing helix chain 'd' and resid 12 through 38 Processing helix chain 'd' and resid 42 through 51 Processing helix chain 'e' and resid 13 through 46 Processing helix chain 'f' and resid 2 through 10 removed outlier: 4.425A pdb=" N TYR f 5 " --> pdb=" O SER f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 38 Processing helix chain 'f' and resid 42 through 51 Processing helix chain 'g' and resid 13 through 46 Processing helix chain 'i' and resid 3 through 10 Processing helix chain 'i' and resid 12 through 38 Processing helix chain 'i' and resid 42 through 51 Processing helix chain 'j' and resid 13 through 46 Processing helix chain 'k' and resid 3 through 10 Processing helix chain 'k' and resid 12 through 38 Processing helix chain 'k' and resid 42 through 51 Processing helix chain 'n' and resid 13 through 46 Processing helix chain 'o' and resid 3 through 10 Processing helix chain 'o' and resid 12 through 38 Processing helix chain 'o' and resid 42 through 51 Processing helix chain 'p' and resid 13 through 46 Processing helix chain 'q' and resid 3 through 10 Processing helix chain 'q' and resid 12 through 38 Processing helix chain 'q' and resid 42 through 51 Processing helix chain 'r' and resid 13 through 46 Processing helix chain 's' and resid 3 through 10 Processing helix chain 's' and resid 12 through 38 Processing helix chain 's' and resid 42 through 51 Processing helix chain 't' and resid 13 through 46 Processing helix chain 'u' and resid 3 through 10 removed outlier: 3.562A pdb=" N LYS u 6 " --> pdb=" O LYS u 3 " (cutoff:3.500A) Processing helix chain 'u' and resid 12 through 38 Processing helix chain 'u' and resid 42 through 51 Processing helix chain 'v' and resid 13 through 46 Processing helix chain 'w' and resid 3 through 10 Processing helix chain 'w' and resid 12 through 38 Processing helix chain 'w' and resid 42 through 51 Processing helix chain 'c' and resid 13 through 46 Processing helix chain '5' and resid 4 through 10 removed outlier: 3.615A pdb=" N ILE 5 7 " --> pdb=" O PHE 5 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE 5 10 " --> pdb=" O ILE 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 38 removed outlier: 3.647A pdb=" N THR 5 38 " --> pdb=" O ILE 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 51 Processing helix chain 'z' and resid 13 through 46 Processing helix chain 'b1' and resid 12 through 38 Processing helix chain 'b1' and resid 42 through 51 Processing helix chain '4' and resid 13 through 46 Processing helix chain '6' and resid 3 through 10 Processing helix chain '6' and resid 12 through 38 Processing helix chain 'b8' and resid 13 through 46 Processing helix chain 'b9' and resid 3 through 10 Processing helix chain 'b9' and resid 12 through 38 Processing helix chain 'b9' and resid 42 through 51 Processing helix chain 'b0' and resid 13 through 46 Processing helix chain 'x' and resid 9 through 13 Processing helix chain 'x' and resid 14 through 55 Processing helix chain 'y' and resid 5 through 29 Processing helix chain 'y' and resid 31 through 49 removed outlier: 4.250A pdb=" N GLY y 35 " --> pdb=" O HIS y 31 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR y 49 " --> pdb=" O PHE y 45 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.551A pdb=" N GLN M 11 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.662A pdb=" N PHE H 7 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 62 through 65 Processing sheet with id=AA5, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA6, first strand: chain 'H' and resid 131 through 133 removed outlier: 5.665A pdb=" N VAL H 164 " --> pdb=" O GLU H 182 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU H 182 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP H 166 " --> pdb=" O GLU H 180 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP H 170 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA H 176 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.612A pdb=" N VAL H 153 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'l' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'm' and resid 10 through 13 removed outlier: 6.550A pdb=" N GLN m 11 " --> pdb=" O SER h 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'h' and resid 5 through 7 removed outlier: 3.662A pdb=" N PHE h 7 " --> pdb=" O PHE h 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'h' and resid 62 through 65 Processing sheet with id=AB3, first strand: chain 'h' and resid 87 through 89 Processing sheet with id=AB4, first strand: chain 'h' and resid 131 through 133 removed outlier: 5.665A pdb=" N VAL h 164 " --> pdb=" O GLU h 182 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU h 182 " --> pdb=" O VAL h 164 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP h 166 " --> pdb=" O GLU h 180 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP h 170 " --> pdb=" O ALA h 176 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA h 176 " --> pdb=" O ASP h 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.612A pdb=" N VAL h 153 " --> pdb=" O ALA h 161 " (cutoff:3.500A) 2646 hydrogen bonds defined for protein. 7458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.05 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 11995 1.35 - 1.55: 34061 1.55 - 1.76: 50 1.76 - 1.97: 338 1.97 - 2.18: 256 Bond restraints: 46700 Sorted by residual: bond pdb=" OB3 CDL M 407 " pdb=" PB2 CDL M 407 " ideal model delta sigma weight residual 1.529 1.455 0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" OB3 CDL m 407 " pdb=" PB2 CDL m 407 " ideal model delta sigma weight residual 1.529 1.456 0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" OA3 CDL m 407 " pdb=" PA1 CDL m 407 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" OA3 CDL M 407 " pdb=" PA1 CDL M 407 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" OB3 CDL F 102 " pdb=" PB2 CDL F 102 " ideal model delta sigma weight residual 1.529 1.459 0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 46695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 63687 4.66 - 9.31: 425 9.31 - 13.97: 28 13.97 - 18.62: 2 18.62 - 23.28: 14 Bond angle restraints: 64156 Sorted by residual: angle pdb=" O12 PC1 A 104 " pdb=" P PC1 A 104 " pdb=" O14 PC1 A 104 " ideal model delta sigma weight residual 123.67 100.39 23.28 3.00e+00 1.11e-01 6.02e+01 angle pdb=" O12 PC1 a 104 " pdb=" P PC1 a 104 " pdb=" O14 PC1 a 104 " ideal model delta sigma weight residual 123.67 100.41 23.26 3.00e+00 1.11e-01 6.01e+01 angle pdb=" O12 PC1 h 301 " pdb=" P PC1 h 301 " pdb=" O14 PC1 h 301 " ideal model delta sigma weight residual 123.67 100.85 22.82 3.00e+00 1.11e-01 5.78e+01 angle pdb=" O12 PC1 H 301 " pdb=" P PC1 H 301 " pdb=" O14 PC1 H 301 " ideal model delta sigma weight residual 123.67 100.85 22.82 3.00e+00 1.11e-01 5.78e+01 angle pdb=" O12 PC1 D 101 " pdb=" P PC1 D 101 " pdb=" O14 PC1 D 101 " ideal model delta sigma weight residual 123.67 100.96 22.71 3.00e+00 1.11e-01 5.73e+01 ... (remaining 64151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.57: 24094 31.57 - 63.13: 826 63.13 - 94.70: 94 94.70 - 126.27: 32 126.27 - 157.84: 2 Dihedral angle restraints: 25048 sinusoidal: 11706 harmonic: 13342 Sorted by residual: dihedral pdb=" C27 U10 l 304 " pdb=" C28 U10 l 304 " pdb=" C29 U10 l 304 " pdb=" C31 U10 l 304 " ideal model delta sinusoidal sigma weight residual -178.28 -20.45 -157.84 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C27 U10 L 304 " pdb=" C28 U10 L 304 " pdb=" C29 U10 L 304 " pdb=" C31 U10 L 304 " ideal model delta sinusoidal sigma weight residual -178.28 -20.48 -157.80 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C3M U10 L 305 " pdb=" C3 U10 L 305 " pdb=" O3 U10 L 305 " pdb=" C4 U10 L 305 " ideal model delta sinusoidal sigma weight residual 244.38 125.33 119.05 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 25045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4890 0.048 - 0.096: 1162 0.096 - 0.143: 176 0.143 - 0.191: 6 0.191 - 0.239: 8 Chirality restraints: 6242 Sorted by residual: chirality pdb=" C2C BPH m 404 " pdb=" C1C BPH m 404 " pdb=" C3C BPH m 404 " pdb=" CMC BPH m 404 " both_signs ideal model delta sigma weight residual False -2.81 -2.57 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2C BPH M 404 " pdb=" C1C BPH M 404 " pdb=" C3C BPH M 404 " pdb=" CMC BPH M 404 " both_signs ideal model delta sigma weight residual False -2.81 -2.57 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3C BPH L 303 " pdb=" C2C BPH L 303 " pdb=" C4C BPH L 303 " pdb=" CAC BPH L 303 " both_signs ideal model delta sigma weight residual False 2.83 2.61 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 6239 not shown) Planarity restraints: 7898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BPH m 404 " 0.013 2.00e-02 2.50e+03 4.75e-02 5.07e+01 pdb=" C1D BPH m 404 " 0.015 2.00e-02 2.50e+03 pdb=" C2D BPH m 404 " -0.024 2.00e-02 2.50e+03 pdb=" C3D BPH m 404 " -0.042 2.00e-02 2.50e+03 pdb=" C4D BPH m 404 " -0.024 2.00e-02 2.50e+03 pdb=" CAD BPH m 404 " 0.106 2.00e-02 2.50e+03 pdb=" CHA BPH m 404 " -0.045 2.00e-02 2.50e+03 pdb=" CHD BPH m 404 " 0.044 2.00e-02 2.50e+03 pdb=" CMD BPH m 404 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH M 404 " -0.013 2.00e-02 2.50e+03 4.74e-02 5.05e+01 pdb=" C1D BPH M 404 " -0.014 2.00e-02 2.50e+03 pdb=" C2D BPH M 404 " 0.024 2.00e-02 2.50e+03 pdb=" C3D BPH M 404 " 0.042 2.00e-02 2.50e+03 pdb=" C4D BPH M 404 " 0.023 2.00e-02 2.50e+03 pdb=" CAD BPH M 404 " -0.106 2.00e-02 2.50e+03 pdb=" CHA BPH M 404 " 0.045 2.00e-02 2.50e+03 pdb=" CHD BPH M 404 " -0.044 2.00e-02 2.50e+03 pdb=" CMD BPH M 404 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH l 303 " 0.016 2.00e-02 2.50e+03 3.05e-02 2.10e+01 pdb=" C1D BPH l 303 " 0.007 2.00e-02 2.50e+03 pdb=" C2D BPH l 303 " -0.017 2.00e-02 2.50e+03 pdb=" C3D BPH l 303 " -0.034 2.00e-02 2.50e+03 pdb=" C4D BPH l 303 " -0.015 2.00e-02 2.50e+03 pdb=" CAD BPH l 303 " 0.068 2.00e-02 2.50e+03 pdb=" CHA BPH l 303 " -0.027 2.00e-02 2.50e+03 pdb=" CHD BPH l 303 " 0.025 2.00e-02 2.50e+03 pdb=" CMD BPH l 303 " -0.021 2.00e-02 2.50e+03 ... (remaining 7895 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 856 2.69 - 3.24: 41146 3.24 - 3.80: 78267 3.80 - 4.35: 104984 4.35 - 4.90: 172799 Nonbonded interactions: 398052 Sorted by model distance: nonbonded pdb=" NE2 HIS l 190 " pdb="FE FE2 m 401 " model vdw 2.138 3.080 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE2 M 401 " model vdw 2.138 3.080 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE2 M 401 " model vdw 2.147 3.000 nonbonded pdb=" OE2 GLU m 234 " pdb="FE FE2 m 401 " model vdw 2.147 3.000 nonbonded pdb=" NE2 HIS m 219 " pdb="FE FE2 m 401 " model vdw 2.163 3.080 ... (remaining 398047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = (chain '0' and resid 8 through 49) selection = (chain '8' and resid 8 through 49) selection = (chain 'B' and resid 8 through 49) selection = (chain 'C' and resid 8 through 49) selection = (chain 'E' and resid 8 through 49) selection = (chain 'G' and resid 8 through 49) selection = (chain 'J' and resid 8 through 49) selection = (chain 'N' and resid 8 through 49) selection = (chain 'P' and resid 8 through 49) selection = (chain 'R' and resid 8 through 49) selection = (chain 'T' and resid 8 through 49) selection = (chain 'V' and resid 8 through 49) selection = (chain 'Z' and resid 8 through 49) selection = (chain 'b' and resid 8 through 49) selection = (chain 'b0' and resid 8 through 49) selection = (chain 'b8' and resid 8 through 49) selection = (chain 'c' and resid 8 through 49) selection = (chain 'e' and resid 8 through 49) selection = (chain 'g' and resid 8 through 49) selection = (chain 'j' and resid 8 through 49) selection = (chain 'n' and resid 8 through 49) selection = (chain 'p' and resid 8 through 49) selection = (chain 'r' and resid 8 through 49) selection = (chain 't' and resid 8 through 49) selection = (chain 'v' and resid 8 through 49) selection = (chain 'z' and resid 8 through 49) } ncs_group { reference = (chain '1' and resid 8 through 48) selection = (chain '3' and resid 8 through 48) selection = (chain '5' and resid 8 through 48) selection = (chain '6' and resid 8 through 48) selection = (chain '7' and resid 8 through 48) selection = (chain 'I' and resid 8 through 48) selection = (chain 'K' and resid 8 through 48) selection = (chain 'O' and resid 8 through 48) selection = (chain 'U' and resid 8 through 48) selection = (chain 'W' and resid 8 through 48) selection = (chain 'b1' and resid 8 through 48) selection = (chain 'i' and resid 8 through 48) selection = (chain 'k' and resid 8 through 48) selection = (chain 'o' and resid 8 through 48) selection = (chain 'u' and resid 8 through 48) selection = (chain 'w' and resid 8 through 48) } ncs_group { reference = chain '2' selection = chain '4' } ncs_group { reference = (chain '9' and resid 1 through 55) selection = (chain 'A' and resid 1 through 55) selection = (chain 'D' and resid 1 through 55) selection = (chain 'F' and resid 1 through 55) selection = (chain 'Q' and resid 1 through 55) selection = (chain 'S' and resid 1 through 55) selection = (chain 'a' and resid 1 through 55) selection = (chain 'b9' and resid 1 through 55) selection = (chain 'd' and resid 1 through 55) selection = (chain 'f' and resid 1 through 55) selection = (chain 'q' and resid 1 through 55) selection = (chain 's' and resid 1 through 55) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'Y' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.850 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.176 46764 Z= 0.578 Angle : 0.959 23.281 64156 Z= 0.376 Chirality : 0.040 0.239 6242 Planarity : 0.004 0.047 7898 Dihedral : 15.584 157.836 16472 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.37 % Allowed : 3.04 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.88 (0.12), residues: 4482 helix: 2.64 (0.09), residues: 2976 sheet: -0.81 (0.74), residues: 48 loop : 0.50 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 46 TYR 0.013 0.001 TYR m 198 PHE 0.018 0.001 PHE h 20 TRP 0.017 0.002 TRP l 263 HIS 0.009 0.001 HIS l 153 Details of bonding type rmsd covalent geometry : bond 0.00708 (46700) covalent geometry : angle 0.95935 (64156) hydrogen bonds : bond 0.11308 ( 2642) hydrogen bonds : angle 4.22794 ( 7458) Misc. bond : bond 0.12463 ( 64) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 871 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 168 MET cc_start: 0.8870 (mmm) cc_final: 0.8598 (mmm) REVERT: M 216 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8933 (t80) REVERT: H 134 MET cc_start: 0.7995 (ttp) cc_final: 0.7640 (ttp) REVERT: D 5 TYR cc_start: 0.9034 (p90) cc_final: 0.8715 (p90) REVERT: E 13 THR cc_start: 0.8286 (p) cc_final: 0.7940 (t) REVERT: F 15 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.7096 (mtm110) REVERT: G 25 MET cc_start: 0.8809 (mmm) cc_final: 0.8522 (mmt) REVERT: O 11 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: W 38 THR cc_start: 0.7978 (p) cc_final: 0.7614 (t) REVERT: C 25 MET cc_start: 0.7014 (mmm) cc_final: 0.6740 (tpp) REVERT: 8 25 MET cc_start: 0.8875 (mmm) cc_final: 0.8595 (mmm) REVERT: m 38 LEU cc_start: 0.9103 (tp) cc_final: 0.8896 (tp) REVERT: m 110 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7745 (mptt) REVERT: m 168 MET cc_start: 0.8878 (mmm) cc_final: 0.8529 (mmm) REVERT: h 134 MET cc_start: 0.7972 (ttp) cc_final: 0.7605 (ttp) REVERT: d 5 TYR cc_start: 0.9035 (p90) cc_final: 0.8727 (p90) REVERT: e 13 THR cc_start: 0.8299 (p) cc_final: 0.7948 (t) REVERT: f 15 ARG cc_start: 0.7521 (mtt-85) cc_final: 0.7122 (mtm110) REVERT: g 25 MET cc_start: 0.8811 (mmm) cc_final: 0.8529 (mmt) REVERT: n 14 ASP cc_start: 0.7638 (t70) cc_final: 0.7376 (t0) REVERT: o 11 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: c 25 MET cc_start: 0.6961 (mmm) cc_final: 0.6692 (tpp) REVERT: b8 25 MET cc_start: 0.8869 (mmm) cc_final: 0.8581 (mmm) outliers start: 14 outliers final: 1 residues processed: 883 average time/residue: 0.5952 time to fit residues: 663.1154 Evaluate side-chains 693 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 689 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain o residue 11 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN B 16 GLN F 20 GLN J 16 GLN K 20 GLN N 16 GLN O 20 GLN Q 20 GLN ** V 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN 9 52 ASN X 10 HIS X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 77 GLN b 16 GLN f 20 GLN j 16 GLN k 20 GLN n 16 GLN o 20 GLN q 20 GLN r 16 GLN t 16 GLN ** v 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN b9 52 ASN x 10 HIS x 66 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105525 restraints weight = 54110.455| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.35 r_work: 0.2792 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 46764 Z= 0.265 Angle : 0.729 14.495 64156 Z= 0.304 Chirality : 0.042 0.165 6242 Planarity : 0.004 0.045 7898 Dihedral : 17.069 129.741 8438 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.22 % Allowed : 10.59 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.50 (0.12), residues: 4482 helix: 2.34 (0.09), residues: 2984 sheet: -0.83 (0.76), residues: 48 loop : 0.36 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 15 TYR 0.018 0.002 TYR q 41 PHE 0.023 0.002 PHE l 216 TRP 0.020 0.002 TRP m 252 HIS 0.011 0.002 HIS M 266 Details of bonding type rmsd covalent geometry : bond 0.00629 (46700) covalent geometry : angle 0.72868 (64156) hydrogen bonds : bond 0.05352 ( 2642) hydrogen bonds : angle 3.99449 ( 7458) Misc. bond : bond 0.00472 ( 64) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 712 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 155 ASP cc_start: 0.9046 (m-30) cc_final: 0.8764 (m-30) REVERT: L 202 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8114 (ttmm) REVERT: M 100 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: M 168 MET cc_start: 0.9280 (mmm) cc_final: 0.9008 (mmm) REVERT: H 1 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8187 (ttp) REVERT: H 43 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7698 (mm-30) REVERT: H 134 MET cc_start: 0.8273 (ttp) cc_final: 0.7679 (ttp) REVERT: H 177 ARG cc_start: 0.8537 (mtt-85) cc_final: 0.8281 (mmt-90) REVERT: A 30 MET cc_start: 0.9023 (ttt) cc_final: 0.8733 (ttt) REVERT: D 5 TYR cc_start: 0.9107 (p90) cc_final: 0.8770 (p90) REVERT: E 13 THR cc_start: 0.8353 (p) cc_final: 0.7579 (t) REVERT: E 15 GLU cc_start: 0.8139 (mp0) cc_final: 0.7757 (mp0) REVERT: F 15 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.6914 (mtm110) REVERT: G 46 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8228 (mtt180) REVERT: N 20 LEU cc_start: 0.8942 (tp) cc_final: 0.8632 (tm) REVERT: N 23 VAL cc_start: 0.9060 (t) cc_final: 0.8838 (p) REVERT: O 9 MET cc_start: 0.8189 (mmt) cc_final: 0.7985 (mmt) REVERT: O 11 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: P 12 LEU cc_start: 0.7878 (mp) cc_final: 0.7428 (mt) REVERT: P 36 ILE cc_start: 0.9195 (mt) cc_final: 0.8992 (mp) REVERT: W 30 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7470 (ptt) REVERT: X 28 MET cc_start: 0.8531 (tpt) cc_final: 0.8128 (mmm) REVERT: X 61 GLN cc_start: 0.8131 (pt0) cc_final: 0.7567 (tt0) REVERT: l 155 ASP cc_start: 0.8986 (m-30) cc_final: 0.8691 (m-30) REVERT: l 202 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8137 (ttmm) REVERT: m 100 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7914 (pm20) REVERT: m 110 LYS cc_start: 0.8348 (mtmm) cc_final: 0.7854 (mptp) REVERT: m 168 MET cc_start: 0.9294 (mmm) cc_final: 0.9028 (mmm) REVERT: h 1 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8240 (ttp) REVERT: h 35 ASN cc_start: 0.8569 (m110) cc_final: 0.8368 (m-40) REVERT: h 43 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: h 134 MET cc_start: 0.8254 (ttp) cc_final: 0.7665 (ttp) REVERT: a 3 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8618 (mtpt) REVERT: a 30 MET cc_start: 0.9018 (ttt) cc_final: 0.8731 (ttt) REVERT: d 5 TYR cc_start: 0.9107 (p90) cc_final: 0.8763 (p90) REVERT: e 13 THR cc_start: 0.8428 (p) cc_final: 0.7645 (t) REVERT: e 15 GLU cc_start: 0.8158 (mp0) cc_final: 0.7773 (mp0) REVERT: f 15 ARG cc_start: 0.8020 (mtt-85) cc_final: 0.6904 (mtm110) REVERT: n 14 ASP cc_start: 0.7998 (t70) cc_final: 0.7585 (t0) REVERT: n 20 LEU cc_start: 0.8936 (tp) cc_final: 0.8639 (tm) REVERT: n 23 VAL cc_start: 0.9036 (t) cc_final: 0.8819 (p) REVERT: o 11 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: p 12 LEU cc_start: 0.7889 (mp) cc_final: 0.7442 (mt) REVERT: w 30 MET cc_start: 0.8028 (ttp) cc_final: 0.7793 (ptp) REVERT: x 28 MET cc_start: 0.8491 (tpt) cc_final: 0.8120 (mmm) REVERT: x 61 GLN cc_start: 0.8079 (pt0) cc_final: 0.7535 (tt0) outliers start: 123 outliers final: 44 residues processed: 759 average time/residue: 0.6034 time to fit residues: 577.7703 Evaluate side-chains 721 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 664 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 202 LYS Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain 3 residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 202 LYS Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 100 GLU Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 315 optimal weight: 0.4980 chunk 215 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 260 optimal weight: 0.7980 chunk 407 optimal weight: 0.4980 chunk 166 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN K 20 GLN O 20 GLN P 16 GLN Q 20 GLN T 16 GLN 8 18 GLN 9 52 ASN X 18 ASN ** X 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN n 16 GLN p 16 GLN q 20 GLN r 16 GLN t 16 GLN b9 52 ASN x 18 ASN ** x 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.148545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109031 restraints weight = 53884.551| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.35 r_work: 0.2857 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 46764 Z= 0.139 Angle : 0.612 15.006 64156 Z= 0.255 Chirality : 0.037 0.133 6242 Planarity : 0.003 0.039 7898 Dihedral : 16.322 122.604 8434 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.73 % Allowed : 11.40 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.67 (0.12), residues: 4482 helix: 2.51 (0.09), residues: 2994 sheet: -0.71 (0.77), residues: 48 loop : 0.31 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG o 15 TYR 0.019 0.001 TYR S 5 PHE 0.017 0.001 PHE h 20 TRP 0.017 0.001 TRP m 252 HIS 0.009 0.001 HIS M 266 Details of bonding type rmsd covalent geometry : bond 0.00310 (46700) covalent geometry : angle 0.61200 (64156) hydrogen bonds : bond 0.04697 ( 2642) hydrogen bonds : angle 3.80570 ( 7458) Misc. bond : bond 0.00278 ( 64) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 726 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 23 ASP cc_start: 0.9280 (t70) cc_final: 0.8953 (t0) REVERT: L 139 MET cc_start: 0.9421 (mtp) cc_final: 0.9105 (mtm) REVERT: L 155 ASP cc_start: 0.9035 (m-30) cc_final: 0.8746 (m-30) REVERT: M 100 GLU cc_start: 0.8123 (pm20) cc_final: 0.7844 (pm20) REVERT: M 168 MET cc_start: 0.9260 (mmm) cc_final: 0.9034 (mmm) REVERT: M 216 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.9154 (t80) REVERT: H 43 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: H 134 MET cc_start: 0.8119 (ttp) cc_final: 0.7596 (ttp) REVERT: A 30 MET cc_start: 0.8936 (ttt) cc_final: 0.8648 (ttp) REVERT: D 5 TYR cc_start: 0.9053 (p90) cc_final: 0.8466 (p90) REVERT: D 38 THR cc_start: 0.8711 (p) cc_final: 0.8439 (p) REVERT: E 13 THR cc_start: 0.8305 (p) cc_final: 0.7506 (t) REVERT: E 14 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7747 (t70) REVERT: E 15 GLU cc_start: 0.8116 (mp0) cc_final: 0.7753 (mp0) REVERT: F 9 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8768 (mmm) REVERT: F 15 ARG cc_start: 0.8011 (mtt-85) cc_final: 0.6848 (mtm110) REVERT: I 3 LYS cc_start: 0.8798 (mttt) cc_final: 0.8557 (mtmt) REVERT: I 6 LYS cc_start: 0.8926 (mtpp) cc_final: 0.8550 (mtmm) REVERT: I 9 MET cc_start: 0.9009 (mtm) cc_final: 0.8741 (mtm) REVERT: I 51 TYR cc_start: 0.8898 (m-80) cc_final: 0.8656 (m-80) REVERT: N 20 LEU cc_start: 0.8975 (tp) cc_final: 0.8635 (tm) REVERT: O 11 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: P 16 GLN cc_start: 0.8039 (pt0) cc_final: 0.7705 (pt0) REVERT: Q 9 MET cc_start: 0.8476 (mtm) cc_final: 0.8143 (mtt) REVERT: V 25 MET cc_start: 0.8294 (tpp) cc_final: 0.7654 (mmm) REVERT: W 30 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7449 (ptt) REVERT: 8 15 GLU cc_start: 0.7988 (pm20) cc_final: 0.7782 (pm20) REVERT: X 28 MET cc_start: 0.8462 (tpt) cc_final: 0.8102 (mmm) REVERT: X 61 GLN cc_start: 0.7929 (pt0) cc_final: 0.7452 (tt0) REVERT: l 139 MET cc_start: 0.9384 (mtp) cc_final: 0.9097 (mtm) REVERT: l 155 ASP cc_start: 0.8989 (m-30) cc_final: 0.8693 (m-30) REVERT: m 100 GLU cc_start: 0.8140 (pm20) cc_final: 0.7870 (pm20) REVERT: m 110 LYS cc_start: 0.8312 (mtmm) cc_final: 0.7850 (mptp) REVERT: m 168 MET cc_start: 0.9264 (mmm) cc_final: 0.9036 (mmm) REVERT: m 216 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.9048 (t80) REVERT: h 43 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: h 134 MET cc_start: 0.8106 (ttp) cc_final: 0.7586 (ttp) REVERT: a 30 MET cc_start: 0.8939 (ttt) cc_final: 0.8648 (ttp) REVERT: d 5 TYR cc_start: 0.9053 (p90) cc_final: 0.8461 (p90) REVERT: d 38 THR cc_start: 0.8715 (p) cc_final: 0.8443 (p) REVERT: e 13 THR cc_start: 0.8302 (p) cc_final: 0.7768 (t) REVERT: e 14 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7769 (t70) REVERT: f 6 LYS cc_start: 0.8732 (mttp) cc_final: 0.8473 (mttp) REVERT: f 9 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8746 (mmm) REVERT: f 15 ARG cc_start: 0.8016 (mtt-85) cc_final: 0.6856 (mtm110) REVERT: i 3 LYS cc_start: 0.8814 (mttt) cc_final: 0.8562 (mtmt) REVERT: i 6 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8523 (mtmm) REVERT: i 9 MET cc_start: 0.8989 (mtm) cc_final: 0.8718 (mtm) REVERT: i 51 TYR cc_start: 0.8896 (m-80) cc_final: 0.8640 (m-80) REVERT: n 20 LEU cc_start: 0.8970 (tp) cc_final: 0.8633 (tm) REVERT: o 6 LYS cc_start: 0.8544 (mtpp) cc_final: 0.8334 (mttp) REVERT: o 11 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7496 (m-80) REVERT: p 16 GLN cc_start: 0.8117 (pt0) cc_final: 0.7809 (pt0) REVERT: p 36 ILE cc_start: 0.9213 (mt) cc_final: 0.8995 (mp) REVERT: q 9 MET cc_start: 0.8465 (mtm) cc_final: 0.8141 (mtt) REVERT: c 25 MET cc_start: 0.6352 (tpp) cc_final: 0.6141 (tpp) REVERT: x 28 MET cc_start: 0.8465 (tpt) cc_final: 0.8103 (mmm) REVERT: x 61 GLN cc_start: 0.7839 (pt0) cc_final: 0.7389 (tt0) outliers start: 104 outliers final: 34 residues processed: 766 average time/residue: 0.5460 time to fit residues: 529.9457 Evaluate side-chains 723 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 678 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain 9 residue 30 MET Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain b9 residue 30 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 123 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 267 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN K 20 GLN O 20 GLN T 16 GLN 9 52 ASN X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN t 16 GLN b9 52 ASN x 18 ASN x 66 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.147571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.108032 restraints weight = 53993.717| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.36 r_work: 0.2837 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 46764 Z= 0.173 Angle : 0.642 14.541 64156 Z= 0.267 Chirality : 0.038 0.183 6242 Planarity : 0.003 0.039 7898 Dihedral : 16.147 121.606 8434 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.70 % Allowed : 12.24 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.58 (0.12), residues: 4482 helix: 2.44 (0.09), residues: 2990 sheet: -0.67 (0.77), residues: 48 loop : 0.27 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG o 15 TYR 0.016 0.001 TYR J 24 PHE 0.018 0.001 PHE L 216 TRP 0.018 0.001 TRP M 252 HIS 0.009 0.001 HIS M 266 Details of bonding type rmsd covalent geometry : bond 0.00403 (46700) covalent geometry : angle 0.64185 (64156) hydrogen bonds : bond 0.04740 ( 2642) hydrogen bonds : angle 3.81139 ( 7458) Misc. bond : bond 0.00324 ( 64) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 700 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 23 ASP cc_start: 0.9265 (t70) cc_final: 0.8943 (t0) REVERT: L 72 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: L 139 MET cc_start: 0.9433 (mtp) cc_final: 0.9148 (mtm) REVERT: L 155 ASP cc_start: 0.9030 (m-30) cc_final: 0.8750 (m-30) REVERT: L 202 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8143 (ttmm) REVERT: M 100 GLU cc_start: 0.8140 (pm20) cc_final: 0.7896 (pm20) REVERT: M 168 MET cc_start: 0.9268 (mmm) cc_final: 0.9013 (mmm) REVERT: H 43 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: H 134 MET cc_start: 0.8146 (ttp) cc_final: 0.7618 (ttp) REVERT: A 1 MET cc_start: 0.5619 (OUTLIER) cc_final: 0.4269 (mmt) REVERT: A 30 MET cc_start: 0.8947 (ttt) cc_final: 0.8642 (ttt) REVERT: D 5 TYR cc_start: 0.9064 (p90) cc_final: 0.8412 (p90) REVERT: D 38 THR cc_start: 0.8691 (p) cc_final: 0.8398 (p) REVERT: E 13 THR cc_start: 0.8382 (p) cc_final: 0.7826 (t) REVERT: E 14 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7776 (t70) REVERT: F 15 ARG cc_start: 0.7967 (mtt-85) cc_final: 0.6819 (mtm110) REVERT: G 46 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8240 (mmm160) REVERT: I 9 MET cc_start: 0.9037 (mtm) cc_final: 0.8758 (mtm) REVERT: I 51 TYR cc_start: 0.8912 (m-80) cc_final: 0.8663 (m-80) REVERT: N 20 LEU cc_start: 0.8945 (tp) cc_final: 0.8660 (tm) REVERT: O 11 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: Q 9 MET cc_start: 0.8470 (mtm) cc_final: 0.8162 (mtt) REVERT: T 42 VAL cc_start: 0.9135 (t) cc_final: 0.8911 (t) REVERT: W 30 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7538 (ptt) REVERT: 3 9 MET cc_start: 0.3859 (mmm) cc_final: 0.3604 (mmm) REVERT: 8 15 GLU cc_start: 0.8012 (pm20) cc_final: 0.7785 (pm20) REVERT: X 61 GLN cc_start: 0.7908 (pt0) cc_final: 0.7528 (tt0) REVERT: l 72 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: l 155 ASP cc_start: 0.8990 (m-30) cc_final: 0.8704 (m-30) REVERT: l 202 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8099 (ttmm) REVERT: m 100 GLU cc_start: 0.8132 (pm20) cc_final: 0.7886 (pm20) REVERT: m 110 LYS cc_start: 0.8372 (mtmm) cc_final: 0.7901 (mptp) REVERT: m 168 MET cc_start: 0.9274 (mmm) cc_final: 0.9018 (mmm) REVERT: m 216 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.9018 (t80) REVERT: h 43 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: h 134 MET cc_start: 0.8136 (ttp) cc_final: 0.7614 (ttp) REVERT: a 1 MET cc_start: 0.5702 (OUTLIER) cc_final: 0.4141 (mmt) REVERT: a 30 MET cc_start: 0.8953 (ttt) cc_final: 0.8647 (ttt) REVERT: d 5 TYR cc_start: 0.9065 (p90) cc_final: 0.8400 (p90) REVERT: d 38 THR cc_start: 0.8693 (p) cc_final: 0.8399 (p) REVERT: e 13 THR cc_start: 0.8394 (p) cc_final: 0.7700 (t) REVERT: e 14 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7753 (t70) REVERT: e 15 GLU cc_start: 0.8114 (mp0) cc_final: 0.7779 (mp0) REVERT: f 6 LYS cc_start: 0.8735 (mttp) cc_final: 0.8445 (mttp) REVERT: f 9 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8746 (mmm) REVERT: f 15 ARG cc_start: 0.7965 (mtt-85) cc_final: 0.6820 (mtm110) REVERT: i 9 MET cc_start: 0.9047 (mtm) cc_final: 0.8771 (mtm) REVERT: i 51 TYR cc_start: 0.8916 (m-80) cc_final: 0.8655 (m-80) REVERT: n 20 LEU cc_start: 0.8924 (tp) cc_final: 0.8645 (tm) REVERT: o 6 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8174 (mttp) REVERT: o 11 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: q 9 MET cc_start: 0.8475 (mtm) cc_final: 0.8169 (mtt) REVERT: v 25 MET cc_start: 0.8255 (tpp) cc_final: 0.7861 (mmm) REVERT: 5 9 MET cc_start: 0.4294 (mmm) cc_final: 0.3214 (mmm) REVERT: x 61 GLN cc_start: 0.7958 (pt0) cc_final: 0.7511 (tt0) outliers start: 103 outliers final: 50 residues processed: 738 average time/residue: 0.4891 time to fit residues: 457.8095 Evaluate side-chains 739 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 673 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 202 LYS Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain 3 residue 45 GLU Chi-restraints excluded: chain 9 residue 30 MET Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 202 LYS Chi-restraints excluded: chain l residue 210 ASP Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain b9 residue 30 MET Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 135 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 349 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 243 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 433 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN K 20 GLN O 20 GLN Q 20 GLN T 16 GLN 9 52 ASN X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN q 20 GLN t 16 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108610 restraints weight = 53752.904| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.34 r_work: 0.2831 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 46764 Z= 0.160 Angle : 0.626 14.729 64156 Z= 0.261 Chirality : 0.038 0.170 6242 Planarity : 0.003 0.038 7898 Dihedral : 15.987 121.972 8434 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.96 % Allowed : 12.97 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.62 (0.12), residues: 4482 helix: 2.46 (0.09), residues: 2994 sheet: -0.68 (0.76), residues: 48 loop : 0.31 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG o 15 TYR 0.017 0.001 TYR j 24 PHE 0.018 0.001 PHE h 20 TRP 0.017 0.001 TRP M 252 HIS 0.009 0.001 HIS m 266 Details of bonding type rmsd covalent geometry : bond 0.00369 (46700) covalent geometry : angle 0.62557 (64156) hydrogen bonds : bond 0.04676 ( 2642) hydrogen bonds : angle 3.78389 ( 7458) Misc. bond : bond 0.00296 ( 64) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 700 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ASP cc_start: 0.9260 (t70) cc_final: 0.8944 (t0) REVERT: L 72 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: L 139 MET cc_start: 0.9438 (mtp) cc_final: 0.9143 (mtm) REVERT: L 155 ASP cc_start: 0.9032 (m-30) cc_final: 0.8757 (m-30) REVERT: L 202 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8134 (ttmm) REVERT: M 100 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: M 168 MET cc_start: 0.9256 (mmm) cc_final: 0.9001 (mmm) REVERT: M 216 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.9037 (t80) REVERT: H 43 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: H 134 MET cc_start: 0.8137 (ttp) cc_final: 0.7620 (ttp) REVERT: A 1 MET cc_start: 0.5689 (OUTLIER) cc_final: 0.4021 (mmt) REVERT: A 30 MET cc_start: 0.8953 (ttt) cc_final: 0.8648 (ttt) REVERT: D 5 TYR cc_start: 0.9062 (p90) cc_final: 0.8392 (p90) REVERT: D 38 THR cc_start: 0.8673 (p) cc_final: 0.8383 (p) REVERT: E 13 THR cc_start: 0.8375 (p) cc_final: 0.7682 (t) REVERT: E 14 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7789 (t70) REVERT: E 15 GLU cc_start: 0.8101 (mp0) cc_final: 0.7783 (mp0) REVERT: F 9 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8760 (mmm) REVERT: F 15 ARG cc_start: 0.7945 (mtt-85) cc_final: 0.6794 (mtm110) REVERT: I 6 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8537 (mtmm) REVERT: I 9 MET cc_start: 0.8970 (mtm) cc_final: 0.8716 (mtm) REVERT: I 51 TYR cc_start: 0.8903 (m-80) cc_final: 0.8685 (m-80) REVERT: N 20 LEU cc_start: 0.8950 (tp) cc_final: 0.8648 (tm) REVERT: O 9 MET cc_start: 0.8441 (mmm) cc_final: 0.7993 (mmt) REVERT: O 11 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: Q 9 MET cc_start: 0.8485 (mtm) cc_final: 0.8190 (mtt) REVERT: T 42 VAL cc_start: 0.9109 (t) cc_final: 0.8881 (t) REVERT: V 25 MET cc_start: 0.8243 (tpp) cc_final: 0.7575 (mmm) REVERT: W 30 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7451 (ptt) REVERT: X 61 GLN cc_start: 0.7989 (pt0) cc_final: 0.7615 (tt0) REVERT: X 66 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8013 (p0) REVERT: l 72 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8005 (pt0) REVERT: l 139 MET cc_start: 0.9228 (mtp) cc_final: 0.8980 (mtm) REVERT: l 155 ASP cc_start: 0.8996 (m-30) cc_final: 0.8727 (m-30) REVERT: l 202 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8098 (ttmm) REVERT: m 100 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: m 110 LYS cc_start: 0.8374 (mtmm) cc_final: 0.7903 (mptp) REVERT: m 168 MET cc_start: 0.9260 (mmm) cc_final: 0.9003 (mmm) REVERT: m 216 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.9024 (t80) REVERT: h 43 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: h 134 MET cc_start: 0.8119 (ttp) cc_final: 0.7611 (ttp) REVERT: a 1 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.3817 (mmt) REVERT: a 30 MET cc_start: 0.8941 (ttt) cc_final: 0.8638 (ttt) REVERT: d 5 TYR cc_start: 0.9061 (p90) cc_final: 0.8388 (p90) REVERT: d 38 THR cc_start: 0.8734 (p) cc_final: 0.8488 (p) REVERT: e 13 THR cc_start: 0.8367 (p) cc_final: 0.7680 (t) REVERT: e 14 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7759 (t70) REVERT: e 15 GLU cc_start: 0.8107 (mp0) cc_final: 0.7771 (mp0) REVERT: f 6 LYS cc_start: 0.8729 (mttp) cc_final: 0.8490 (mttp) REVERT: f 9 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8746 (mmm) REVERT: f 15 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.6790 (mtm110) REVERT: i 6 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8503 (mtmm) REVERT: i 9 MET cc_start: 0.8967 (mtm) cc_final: 0.8714 (mtm) REVERT: i 51 TYR cc_start: 0.8895 (m-80) cc_final: 0.8654 (m-80) REVERT: k 9 MET cc_start: 0.8525 (mtm) cc_final: 0.8223 (mmm) REVERT: n 20 LEU cc_start: 0.8930 (tp) cc_final: 0.8640 (tm) REVERT: o 6 LYS cc_start: 0.8366 (mtpp) cc_final: 0.8144 (mttt) REVERT: o 9 MET cc_start: 0.8366 (mmm) cc_final: 0.8071 (mmm) REVERT: o 11 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: q 9 MET cc_start: 0.8477 (mtm) cc_final: 0.8182 (mtt) REVERT: t 42 VAL cc_start: 0.9105 (t) cc_final: 0.8882 (t) REVERT: v 25 MET cc_start: 0.8203 (tpp) cc_final: 0.7563 (mmm) REVERT: 5 9 MET cc_start: 0.4310 (mmm) cc_final: 0.4016 (mmm) REVERT: x 61 GLN cc_start: 0.7945 (pt0) cc_final: 0.7604 (tt0) REVERT: x 66 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8020 (p0) outliers start: 113 outliers final: 53 residues processed: 744 average time/residue: 0.4287 time to fit residues: 405.6893 Evaluate side-chains 747 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 673 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 202 LYS Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 242 MET Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 202 LYS Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 100 GLU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 105 MET Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 242 MET Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain b9 residue 30 MET Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 4 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 285 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 401 optimal weight: 7.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 60 ASN M 25 ASN K 20 GLN O 20 GLN T 16 GLN 8 18 GLN 9 52 ASN X 18 ASN X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN o 20 GLN t 16 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108706 restraints weight = 53915.072| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.34 r_work: 0.2835 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 46764 Z= 0.160 Angle : 0.634 14.673 64156 Z= 0.263 Chirality : 0.038 0.155 6242 Planarity : 0.003 0.038 7898 Dihedral : 15.889 122.010 8434 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.70 % Allowed : 13.86 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.67 (0.12), residues: 4482 helix: 2.51 (0.09), residues: 2982 sheet: -0.65 (0.76), residues: 48 loop : 0.35 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 15 TYR 0.016 0.001 TYR J 24 PHE 0.018 0.001 PHE h 20 TRP 0.017 0.001 TRP M 252 HIS 0.008 0.001 HIS M 266 Details of bonding type rmsd covalent geometry : bond 0.00371 (46700) covalent geometry : angle 0.63412 (64156) hydrogen bonds : bond 0.04657 ( 2642) hydrogen bonds : angle 3.77376 ( 7458) Misc. bond : bond 0.00296 ( 64) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 691 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 23 ASP cc_start: 0.9257 (t70) cc_final: 0.8959 (t0) REVERT: L 72 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: L 139 MET cc_start: 0.9430 (mtp) cc_final: 0.9064 (mtm) REVERT: L 155 ASP cc_start: 0.9020 (m-30) cc_final: 0.8745 (m-30) REVERT: L 202 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8115 (ttmm) REVERT: M 100 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: M 168 MET cc_start: 0.9267 (mmm) cc_final: 0.9000 (mmm) REVERT: M 216 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.9004 (t80) REVERT: M 236 GLU cc_start: 0.8028 (tp30) cc_final: 0.7700 (tp30) REVERT: H 43 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: H 134 MET cc_start: 0.8135 (ttp) cc_final: 0.7618 (ttp) REVERT: A 1 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.4043 (mmt) REVERT: A 3 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8576 (mtpt) REVERT: A 30 MET cc_start: 0.8963 (ttt) cc_final: 0.8659 (ttt) REVERT: D 5 TYR cc_start: 0.9060 (p90) cc_final: 0.8402 (p90) REVERT: D 38 THR cc_start: 0.8734 (p) cc_final: 0.8487 (p) REVERT: E 13 THR cc_start: 0.8453 (p) cc_final: 0.7809 (t) REVERT: E 14 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7799 (t70) REVERT: E 15 GLU cc_start: 0.8114 (mp0) cc_final: 0.7801 (mp0) REVERT: F 6 LYS cc_start: 0.8645 (mttp) cc_final: 0.8410 (mttp) REVERT: F 9 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8781 (mmm) REVERT: F 15 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.6793 (mtm110) REVERT: I 3 LYS cc_start: 0.8843 (mttm) cc_final: 0.8378 (mtmt) REVERT: I 6 LYS cc_start: 0.8994 (mtpp) cc_final: 0.8563 (mtmm) REVERT: I 9 MET cc_start: 0.8963 (mtm) cc_final: 0.8715 (mtm) REVERT: I 51 TYR cc_start: 0.8863 (m-80) cc_final: 0.8619 (m-80) REVERT: N 20 LEU cc_start: 0.8945 (tp) cc_final: 0.8633 (tm) REVERT: O 9 MET cc_start: 0.8505 (mmm) cc_final: 0.8282 (mmm) REVERT: O 11 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: P 16 GLN cc_start: 0.8017 (pt0) cc_final: 0.7796 (pm20) REVERT: P 22 SER cc_start: 0.8122 (p) cc_final: 0.7846 (p) REVERT: Q 9 MET cc_start: 0.8455 (mtm) cc_final: 0.8213 (mtt) REVERT: T 42 VAL cc_start: 0.9115 (t) cc_final: 0.8888 (t) REVERT: V 25 MET cc_start: 0.8193 (tpp) cc_final: 0.7571 (mmm) REVERT: W 30 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7469 (ptt) REVERT: 3 9 MET cc_start: 0.4263 (mmm) cc_final: 0.3815 (mmm) REVERT: X 61 GLN cc_start: 0.7984 (pt0) cc_final: 0.7646 (tt0) REVERT: X 66 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.7889 (p0) REVERT: l 72 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: l 139 MET cc_start: 0.9231 (mtp) cc_final: 0.8994 (mtm) REVERT: l 155 ASP cc_start: 0.8999 (m-30) cc_final: 0.8729 (m-30) REVERT: l 202 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8103 (ttmm) REVERT: m 100 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: m 110 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7928 (mptp) REVERT: m 168 MET cc_start: 0.9260 (mmm) cc_final: 0.8991 (mmm) REVERT: m 216 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.9010 (t80) REVERT: m 236 GLU cc_start: 0.8004 (tp30) cc_final: 0.6993 (tp30) REVERT: h 43 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7388 (mm-30) REVERT: h 134 MET cc_start: 0.8115 (ttp) cc_final: 0.7584 (ttp) REVERT: a 1 MET cc_start: 0.5702 (OUTLIER) cc_final: 0.3803 (mmt) REVERT: a 30 MET cc_start: 0.8957 (ttt) cc_final: 0.8656 (ttt) REVERT: d 5 TYR cc_start: 0.9057 (p90) cc_final: 0.8398 (p90) REVERT: e 13 THR cc_start: 0.8447 (p) cc_final: 0.7821 (t) REVERT: e 14 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7779 (t70) REVERT: e 15 GLU cc_start: 0.8125 (mp0) cc_final: 0.7807 (mp0) REVERT: f 6 LYS cc_start: 0.8733 (mttp) cc_final: 0.8495 (mttp) REVERT: f 9 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8747 (mmm) REVERT: f 15 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.6792 (mtm110) REVERT: i 3 LYS cc_start: 0.8838 (mttm) cc_final: 0.8387 (mtmt) REVERT: i 6 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8502 (mtmm) REVERT: i 9 MET cc_start: 0.8967 (mtm) cc_final: 0.8723 (mtm) REVERT: i 51 TYR cc_start: 0.8867 (m-80) cc_final: 0.8610 (m-80) REVERT: n 20 LEU cc_start: 0.8949 (tp) cc_final: 0.8645 (tm) REVERT: o 9 MET cc_start: 0.8447 (mmm) cc_final: 0.8145 (mmm) REVERT: o 11 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7553 (m-80) REVERT: q 9 MET cc_start: 0.8463 (mtm) cc_final: 0.8200 (mtt) REVERT: t 42 VAL cc_start: 0.9110 (t) cc_final: 0.8883 (t) REVERT: x 61 GLN cc_start: 0.7947 (pt0) cc_final: 0.7646 (tt0) REVERT: x 66 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.7901 (p0) outliers start: 103 outliers final: 57 residues processed: 731 average time/residue: 0.4161 time to fit residues: 389.2705 Evaluate side-chains 748 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 670 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 202 LYS Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 242 MET Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain 3 residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 202 LYS Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 100 GLU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 105 MET Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 242 MET Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 119 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 290 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 25 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN K 20 GLN O 20 GLN T 16 GLN 9 52 ASN X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN o 20 GLN t 16 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106714 restraints weight = 53855.775| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.30 r_work: 0.2807 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 46764 Z= 0.233 Angle : 0.698 14.457 64156 Z= 0.290 Chirality : 0.040 0.158 6242 Planarity : 0.004 0.039 7898 Dihedral : 16.161 121.535 8434 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.04 % Allowed : 13.76 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.45 (0.12), residues: 4482 helix: 2.33 (0.09), residues: 2982 sheet: -0.79 (0.76), residues: 48 loop : 0.29 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 15 TYR 0.018 0.002 TYR q 5 PHE 0.021 0.002 PHE L 216 TRP 0.017 0.002 TRP M 252 HIS 0.008 0.002 HIS M 266 Details of bonding type rmsd covalent geometry : bond 0.00551 (46700) covalent geometry : angle 0.69826 (64156) hydrogen bonds : bond 0.04947 ( 2642) hydrogen bonds : angle 3.89568 ( 7458) Misc. bond : bond 0.00402 ( 64) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 684 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ASP cc_start: 0.9276 (t70) cc_final: 0.8925 (t0) REVERT: L 72 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: L 139 MET cc_start: 0.9438 (mtp) cc_final: 0.9121 (mtm) REVERT: L 155 ASP cc_start: 0.9032 (m-30) cc_final: 0.8757 (m-30) REVERT: L 202 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8118 (ttmm) REVERT: M 100 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: M 168 MET cc_start: 0.9268 (mmm) cc_final: 0.8993 (mmm) REVERT: M 216 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.9032 (t80) REVERT: H 43 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: H 134 MET cc_start: 0.8231 (ttp) cc_final: 0.7676 (ttp) REVERT: A 1 MET cc_start: 0.5704 (OUTLIER) cc_final: 0.4042 (mmt) REVERT: A 30 MET cc_start: 0.8992 (ttt) cc_final: 0.8690 (ttt) REVERT: D 5 TYR cc_start: 0.9087 (p90) cc_final: 0.8391 (p90) REVERT: D 20 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: E 14 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7927 (t70) REVERT: F 15 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.6827 (mtm110) REVERT: I 3 LYS cc_start: 0.8853 (mttm) cc_final: 0.8624 (mtmt) REVERT: I 9 MET cc_start: 0.9032 (mtm) cc_final: 0.8768 (mtm) REVERT: I 51 TYR cc_start: 0.8882 (m-80) cc_final: 0.8633 (m-80) REVERT: N 20 LEU cc_start: 0.8974 (tp) cc_final: 0.8653 (tm) REVERT: O 9 MET cc_start: 0.8502 (mmm) cc_final: 0.8031 (mmt) REVERT: O 11 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: P 16 GLN cc_start: 0.7944 (pt0) cc_final: 0.7664 (pm20) REVERT: P 22 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7841 (p) REVERT: Q 9 MET cc_start: 0.8480 (mtm) cc_final: 0.8275 (mtt) REVERT: T 42 VAL cc_start: 0.9157 (t) cc_final: 0.8935 (t) REVERT: V 25 MET cc_start: 0.8180 (tpp) cc_final: 0.7813 (mmm) REVERT: W 30 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7439 (ptt) REVERT: 3 9 MET cc_start: 0.4125 (mmm) cc_final: 0.3792 (mmm) REVERT: X 61 GLN cc_start: 0.8055 (pt0) cc_final: 0.7767 (tt0) REVERT: X 66 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.7853 (p0) REVERT: l 72 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: l 139 MET cc_start: 0.9258 (mtp) cc_final: 0.9037 (mtm) REVERT: l 155 ASP cc_start: 0.9003 (m-30) cc_final: 0.8729 (m-30) REVERT: l 202 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8115 (ttmm) REVERT: l 205 GLU cc_start: 0.8309 (pt0) cc_final: 0.7798 (pm20) REVERT: m 100 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: m 110 LYS cc_start: 0.8408 (mtmm) cc_final: 0.7859 (mmtt) REVERT: m 168 MET cc_start: 0.9267 (mmm) cc_final: 0.8984 (mmm) REVERT: m 216 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.9129 (t80) REVERT: m 236 GLU cc_start: 0.8057 (tp30) cc_final: 0.7843 (tp30) REVERT: h 43 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: h 134 MET cc_start: 0.8215 (ttp) cc_final: 0.7666 (ttp) REVERT: a 1 MET cc_start: 0.5698 (OUTLIER) cc_final: 0.3829 (mmt) REVERT: a 30 MET cc_start: 0.8974 (ttt) cc_final: 0.8677 (ttt) REVERT: d 5 TYR cc_start: 0.9088 (p90) cc_final: 0.8390 (p90) REVERT: d 20 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8417 (tm-30) REVERT: e 14 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7925 (t70) REVERT: f 15 ARG cc_start: 0.7972 (mtt-85) cc_final: 0.6831 (mtm110) REVERT: i 3 LYS cc_start: 0.8851 (mttm) cc_final: 0.8619 (mtmt) REVERT: i 9 MET cc_start: 0.8982 (mtm) cc_final: 0.8707 (mtm) REVERT: i 51 TYR cc_start: 0.8881 (m-80) cc_final: 0.8613 (m-80) REVERT: n 14 ASP cc_start: 0.7931 (t70) cc_final: 0.7449 (t0) REVERT: n 20 LEU cc_start: 0.8946 (tp) cc_final: 0.8640 (tm) REVERT: o 9 MET cc_start: 0.8477 (mmm) cc_final: 0.7968 (mmt) REVERT: o 11 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: p 16 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7274 (pm20) REVERT: q 9 MET cc_start: 0.8495 (mtm) cc_final: 0.8290 (mtt) REVERT: t 42 VAL cc_start: 0.9157 (t) cc_final: 0.8933 (t) REVERT: v 25 MET cc_start: 0.8307 (mmm) cc_final: 0.7693 (mmm) REVERT: 5 9 MET cc_start: 0.4349 (mmm) cc_final: 0.3940 (mmm) REVERT: x 8 ASN cc_start: 0.8162 (p0) cc_final: 0.7950 (p0) REVERT: x 61 GLN cc_start: 0.7989 (pt0) cc_final: 0.7754 (tt0) REVERT: x 66 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.7876 (p0) outliers start: 116 outliers final: 60 residues processed: 728 average time/residue: 0.4190 time to fit residues: 387.8034 Evaluate side-chains 750 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 667 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 202 LYS Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain 3 residue 45 GLU Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 202 LYS Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 100 GLU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 105 MET Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 16 GLN Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 321 optimal weight: 0.9990 chunk 420 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 303 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 25 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN K 20 GLN N 16 GLN O 20 GLN R 16 GLN T 16 GLN 9 52 ASN X 66 ASN l 60 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN n 16 GLN o 20 GLN r 16 GLN t 16 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108503 restraints weight = 54103.565| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.31 r_work: 0.2837 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 46764 Z= 0.164 Angle : 0.650 15.086 64156 Z= 0.270 Chirality : 0.038 0.153 6242 Planarity : 0.003 0.038 7898 Dihedral : 15.900 122.277 8434 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.65 % Allowed : 14.28 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.55 (0.12), residues: 4482 helix: 2.41 (0.09), residues: 2982 sheet: -0.69 (0.76), residues: 48 loop : 0.31 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 207 TYR 0.021 0.001 TYR J 24 PHE 0.018 0.001 PHE h 20 TRP 0.017 0.001 TRP m 252 HIS 0.008 0.001 HIS M 266 Details of bonding type rmsd covalent geometry : bond 0.00380 (46700) covalent geometry : angle 0.64978 (64156) hydrogen bonds : bond 0.04710 ( 2642) hydrogen bonds : angle 3.81688 ( 7458) Misc. bond : bond 0.00296 ( 64) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 681 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ASP cc_start: 0.9268 (t70) cc_final: 0.8938 (t0) REVERT: L 72 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: L 139 MET cc_start: 0.9424 (mtp) cc_final: 0.9103 (mtm) REVERT: L 155 ASP cc_start: 0.9036 (m-30) cc_final: 0.8758 (m-30) REVERT: L 202 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8109 (ttmm) REVERT: M 100 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: M 168 MET cc_start: 0.9254 (mmm) cc_final: 0.8983 (mmm) REVERT: M 216 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.9030 (t80) REVERT: H 43 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: H 134 MET cc_start: 0.8154 (ttp) cc_final: 0.7649 (ttp) REVERT: A 1 MET cc_start: 0.5647 (OUTLIER) cc_final: 0.3966 (mmt) REVERT: A 30 MET cc_start: 0.8974 (ttt) cc_final: 0.8675 (ttt) REVERT: D 5 TYR cc_start: 0.9068 (p90) cc_final: 0.8448 (p90) REVERT: E 14 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8022 (t70) REVERT: F 6 LYS cc_start: 0.8723 (mttp) cc_final: 0.8488 (mttp) REVERT: F 9 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8783 (mmm) REVERT: F 15 ARG cc_start: 0.7956 (mtt-85) cc_final: 0.6840 (mtm110) REVERT: I 3 LYS cc_start: 0.8839 (mttm) cc_final: 0.8373 (mtmt) REVERT: I 6 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8476 (mtmm) REVERT: I 9 MET cc_start: 0.8926 (mtm) cc_final: 0.8685 (mtm) REVERT: I 51 TYR cc_start: 0.8860 (m-80) cc_final: 0.8616 (m-80) REVERT: N 20 LEU cc_start: 0.8969 (tp) cc_final: 0.8641 (tm) REVERT: O 6 LYS cc_start: 0.8360 (mttp) cc_final: 0.8128 (mtpp) REVERT: O 9 MET cc_start: 0.8505 (mmm) cc_final: 0.7930 (mmt) REVERT: O 11 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: P 16 GLN cc_start: 0.7968 (pt0) cc_final: 0.7728 (pm20) REVERT: T 42 VAL cc_start: 0.9149 (t) cc_final: 0.8923 (t) REVERT: V 25 MET cc_start: 0.8183 (tpp) cc_final: 0.7604 (mmm) REVERT: W 30 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7463 (ptt) REVERT: 3 9 MET cc_start: 0.3977 (mmm) cc_final: 0.3737 (mmm) REVERT: X 8 ASN cc_start: 0.8079 (p0) cc_final: 0.7856 (p0) REVERT: X 61 GLN cc_start: 0.8000 (pt0) cc_final: 0.7747 (tt0) REVERT: X 66 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7910 (p0) REVERT: l 72 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: l 139 MET cc_start: 0.9246 (mtp) cc_final: 0.9025 (mtm) REVERT: l 155 ASP cc_start: 0.9012 (m-30) cc_final: 0.8755 (m-30) REVERT: l 202 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8109 (ttmm) REVERT: l 205 GLU cc_start: 0.8265 (pt0) cc_final: 0.7739 (pm20) REVERT: m 100 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: m 110 LYS cc_start: 0.8404 (mtmm) cc_final: 0.7861 (mmtt) REVERT: m 168 MET cc_start: 0.9253 (mmm) cc_final: 0.8979 (mmm) REVERT: m 216 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.9036 (t80) REVERT: m 236 GLU cc_start: 0.8098 (tp30) cc_final: 0.7845 (tp30) REVERT: h 43 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: h 134 MET cc_start: 0.8120 (ttp) cc_final: 0.7621 (ttp) REVERT: a 1 MET cc_start: 0.5554 (OUTLIER) cc_final: 0.3641 (mmt) REVERT: a 30 MET cc_start: 0.8970 (ttt) cc_final: 0.8675 (ttt) REVERT: d 5 TYR cc_start: 0.9057 (p90) cc_final: 0.8400 (p90) REVERT: e 14 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7933 (t70) REVERT: f 9 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8770 (mmm) REVERT: f 15 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.6848 (mtm110) REVERT: i 3 LYS cc_start: 0.8843 (mttm) cc_final: 0.8380 (mtmt) REVERT: i 6 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8478 (mtmm) REVERT: i 9 MET cc_start: 0.8908 (mtm) cc_final: 0.8666 (mtm) REVERT: i 51 TYR cc_start: 0.8866 (m-80) cc_final: 0.8650 (m-80) REVERT: n 14 ASP cc_start: 0.7936 (t70) cc_final: 0.7461 (t0) REVERT: n 20 LEU cc_start: 0.8954 (tp) cc_final: 0.8639 (tm) REVERT: o 9 MET cc_start: 0.8477 (mmm) cc_final: 0.7984 (mmt) REVERT: o 11 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: p 16 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: r 18 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: t 42 VAL cc_start: 0.9150 (t) cc_final: 0.8924 (t) REVERT: v 25 MET cc_start: 0.8342 (mmm) cc_final: 0.7777 (mmm) REVERT: w 15 ARG cc_start: 0.5091 (OUTLIER) cc_final: 0.4210 (mtp180) REVERT: w 38 THR cc_start: 0.7383 (p) cc_final: 0.7138 (t) REVERT: c 25 MET cc_start: 0.6099 (tpp) cc_final: 0.5631 (tpp) REVERT: 5 9 MET cc_start: 0.4088 (mmm) cc_final: 0.3769 (mmm) REVERT: x 8 ASN cc_start: 0.8161 (p0) cc_final: 0.7928 (p0) REVERT: x 61 GLN cc_start: 0.7977 (pt0) cc_final: 0.7771 (tt0) REVERT: x 66 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7907 (p0) outliers start: 101 outliers final: 50 residues processed: 721 average time/residue: 0.4131 time to fit residues: 378.3855 Evaluate side-chains 745 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 671 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 202 LYS Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain 3 residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 202 LYS Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 100 GLU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 16 GLN Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 15 ARG Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 417 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 189 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 303 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 357 optimal weight: 0.6980 chunk 370 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 25 ASN B 16 GLN K 20 GLN N 16 GLN O 20 GLN R 16 GLN T 16 GLN 9 52 ASN X 66 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN n 16 GLN o 20 GLN r 16 GLN t 16 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108727 restraints weight = 53834.462| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.32 r_work: 0.2841 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 46764 Z= 0.159 Angle : 0.640 14.910 64156 Z= 0.267 Chirality : 0.038 0.157 6242 Planarity : 0.003 0.038 7898 Dihedral : 15.788 122.256 8434 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.36 % Allowed : 14.78 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.56 (0.12), residues: 4482 helix: 2.42 (0.09), residues: 2994 sheet: -0.66 (0.76), residues: 48 loop : 0.30 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 15 TYR 0.020 0.001 TYR J 24 PHE 0.018 0.001 PHE h 20 TRP 0.018 0.001 TRP 3 8 HIS 0.008 0.001 HIS M 266 Details of bonding type rmsd covalent geometry : bond 0.00368 (46700) covalent geometry : angle 0.64000 (64156) hydrogen bonds : bond 0.04674 ( 2642) hydrogen bonds : angle 3.79852 ( 7458) Misc. bond : bond 0.00289 ( 64) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 680 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ASP cc_start: 0.9268 (t70) cc_final: 0.8934 (t0) REVERT: L 72 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8011 (pt0) REVERT: L 139 MET cc_start: 0.9426 (mtp) cc_final: 0.9070 (mtm) REVERT: L 155 ASP cc_start: 0.9005 (m-30) cc_final: 0.8715 (m-30) REVERT: L 202 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8107 (ttmm) REVERT: M 100 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: M 168 MET cc_start: 0.9263 (mmm) cc_final: 0.8989 (mmm) REVERT: M 216 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.9043 (t80) REVERT: H 43 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: H 134 MET cc_start: 0.8103 (ttp) cc_final: 0.7573 (ttp) REVERT: A 1 MET cc_start: 0.5582 (OUTLIER) cc_final: 0.3837 (mmt) REVERT: A 30 MET cc_start: 0.8981 (ttt) cc_final: 0.8677 (ttt) REVERT: D 3 LYS cc_start: 0.8725 (mtpm) cc_final: 0.8377 (ttpt) REVERT: D 5 TYR cc_start: 0.9043 (p90) cc_final: 0.8418 (p90) REVERT: E 14 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8020 (t70) REVERT: E 15 GLU cc_start: 0.8042 (mp0) cc_final: 0.7834 (mp0) REVERT: F 6 LYS cc_start: 0.8653 (mttp) cc_final: 0.8385 (mttp) REVERT: F 9 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8774 (mmm) REVERT: F 15 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.6819 (mtm110) REVERT: I 3 LYS cc_start: 0.8832 (mttm) cc_final: 0.8362 (mtmt) REVERT: I 6 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8471 (mtmm) REVERT: I 9 MET cc_start: 0.8909 (mtm) cc_final: 0.8671 (mtm) REVERT: N 20 LEU cc_start: 0.8969 (tp) cc_final: 0.8640 (tm) REVERT: O 9 MET cc_start: 0.8483 (mmm) cc_final: 0.8003 (mmt) REVERT: O 11 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: P 16 GLN cc_start: 0.7899 (pt0) cc_final: 0.7617 (pm20) REVERT: T 42 VAL cc_start: 0.9143 (t) cc_final: 0.8918 (t) REVERT: V 25 MET cc_start: 0.8173 (tpp) cc_final: 0.7662 (mmm) REVERT: W 30 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7511 (ptt) REVERT: 3 9 MET cc_start: 0.3971 (mmm) cc_final: 0.3750 (mmm) REVERT: X 8 ASN cc_start: 0.8115 (p0) cc_final: 0.7872 (p0) REVERT: X 61 GLN cc_start: 0.7984 (pt0) cc_final: 0.7751 (tt0) REVERT: X 66 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.7865 (p0) REVERT: l 72 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: l 139 MET cc_start: 0.9246 (mtp) cc_final: 0.9018 (mtm) REVERT: l 155 ASP cc_start: 0.9004 (m-30) cc_final: 0.8740 (m-30) REVERT: l 202 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8117 (ttmm) REVERT: m 100 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: m 110 LYS cc_start: 0.8404 (mtmm) cc_final: 0.7854 (mmtt) REVERT: m 168 MET cc_start: 0.9265 (mmm) cc_final: 0.8989 (mmm) REVERT: m 216 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.9043 (t80) REVERT: m 236 GLU cc_start: 0.8078 (tp30) cc_final: 0.7868 (tp30) REVERT: h 43 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: h 134 MET cc_start: 0.8099 (ttp) cc_final: 0.7578 (ttp) REVERT: a 30 MET cc_start: 0.8960 (ttt) cc_final: 0.8660 (ttt) REVERT: d 5 TYR cc_start: 0.9052 (p90) cc_final: 0.8437 (p90) REVERT: e 14 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8059 (t70) REVERT: f 9 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8777 (mmm) REVERT: f 15 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.6824 (mtm110) REVERT: i 3 LYS cc_start: 0.8834 (mttm) cc_final: 0.8359 (mtmt) REVERT: i 6 LYS cc_start: 0.8943 (mtpp) cc_final: 0.8472 (mtmm) REVERT: i 9 MET cc_start: 0.8904 (mtm) cc_final: 0.8666 (mtm) REVERT: i 51 TYR cc_start: 0.8861 (m-80) cc_final: 0.8658 (m-80) REVERT: n 14 ASP cc_start: 0.7888 (t70) cc_final: 0.7424 (t0) REVERT: n 20 LEU cc_start: 0.8954 (tp) cc_final: 0.8634 (tm) REVERT: o 9 MET cc_start: 0.8491 (mmm) cc_final: 0.7999 (mmt) REVERT: o 11 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7514 (m-80) REVERT: p 16 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: r 18 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: t 42 VAL cc_start: 0.9147 (t) cc_final: 0.8918 (t) REVERT: v 25 MET cc_start: 0.8334 (mmm) cc_final: 0.7737 (mmm) REVERT: w 15 ARG cc_start: 0.5103 (OUTLIER) cc_final: 0.4213 (mtp180) REVERT: w 38 THR cc_start: 0.7366 (p) cc_final: 0.7132 (t) REVERT: 5 9 MET cc_start: 0.4110 (mmm) cc_final: 0.3806 (mmm) REVERT: x 8 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7925 (p0) REVERT: x 66 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.7863 (p0) outliers start: 90 outliers final: 53 residues processed: 716 average time/residue: 0.4184 time to fit residues: 381.6731 Evaluate side-chains 744 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 667 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 202 LYS Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain 3 residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 202 LYS Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 100 GLU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 16 GLN Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 15 ARG Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain x residue 8 ASN Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 60 optimal weight: 1.9990 chunk 387 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 319 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 241 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 136 optimal weight: 0.6980 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 25 ASN B 16 GLN K 20 GLN N 16 GLN O 20 GLN R 16 GLN T 16 GLN 9 52 ASN X 66 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN n 16 GLN o 20 GLN r 16 GLN t 16 GLN b9 52 ASN x 61 GLN x 66 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109332 restraints weight = 54038.837| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.32 r_work: 0.2861 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 46764 Z= 0.146 Angle : 0.637 14.913 64156 Z= 0.266 Chirality : 0.037 0.139 6242 Planarity : 0.003 0.038 7898 Dihedral : 15.645 122.498 8434 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.02 % Allowed : 15.17 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.61 (0.12), residues: 4482 helix: 2.46 (0.09), residues: 2994 sheet: -0.61 (0.76), residues: 48 loop : 0.29 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 15 TYR 0.023 0.001 TYR J 24 PHE 0.019 0.001 PHE H 20 TRP 0.017 0.001 TRP 3 8 HIS 0.008 0.001 HIS M 266 Details of bonding type rmsd covalent geometry : bond 0.00334 (46700) covalent geometry : angle 0.63695 (64156) hydrogen bonds : bond 0.04607 ( 2642) hydrogen bonds : angle 3.76977 ( 7458) Misc. bond : bond 0.00260 ( 64) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 685 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ASP cc_start: 0.9261 (t70) cc_final: 0.8969 (t0) REVERT: L 72 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: L 139 MET cc_start: 0.9419 (mtp) cc_final: 0.9103 (mtm) REVERT: L 155 ASP cc_start: 0.8998 (m-30) cc_final: 0.8707 (m-30) REVERT: M 100 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: M 168 MET cc_start: 0.9257 (mmm) cc_final: 0.8987 (mmm) REVERT: M 216 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8941 (t80) REVERT: H 43 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: H 134 MET cc_start: 0.8118 (ttp) cc_final: 0.7577 (ttp) REVERT: A 1 MET cc_start: 0.5558 (OUTLIER) cc_final: 0.3561 (mmt) REVERT: A 30 MET cc_start: 0.8954 (ttt) cc_final: 0.8656 (ttt) REVERT: D 3 LYS cc_start: 0.8741 (mtpm) cc_final: 0.8440 (ttpt) REVERT: D 5 TYR cc_start: 0.9012 (p90) cc_final: 0.8414 (p90) REVERT: E 14 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8113 (t70) REVERT: E 15 GLU cc_start: 0.8057 (mp0) cc_final: 0.7854 (mp0) REVERT: F 6 LYS cc_start: 0.8681 (mttp) cc_final: 0.8430 (mttp) REVERT: F 9 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8788 (mmm) REVERT: F 15 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.6822 (mtm110) REVERT: I 3 LYS cc_start: 0.8825 (mttm) cc_final: 0.8362 (mtmt) REVERT: I 6 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8443 (mtmm) REVERT: I 9 MET cc_start: 0.8903 (mtm) cc_final: 0.8682 (mtm) REVERT: N 20 LEU cc_start: 0.8975 (tp) cc_final: 0.8647 (tm) REVERT: O 6 LYS cc_start: 0.8401 (mttp) cc_final: 0.8100 (mtpt) REVERT: O 9 MET cc_start: 0.8478 (mmm) cc_final: 0.7932 (mmt) REVERT: O 11 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: P 16 GLN cc_start: 0.7920 (pt0) cc_final: 0.7687 (pm20) REVERT: T 42 VAL cc_start: 0.9138 (t) cc_final: 0.8913 (t) REVERT: V 25 MET cc_start: 0.8184 (tpp) cc_final: 0.7649 (mmm) REVERT: W 30 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7471 (ptt) REVERT: Z 25 MET cc_start: 0.6196 (mmm) cc_final: 0.5962 (mmm) REVERT: X 8 ASN cc_start: 0.8120 (p0) cc_final: 0.7895 (p0) REVERT: X 66 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.7740 (p0) REVERT: l 72 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: l 155 ASP cc_start: 0.9003 (m-30) cc_final: 0.8745 (m-30) REVERT: m 100 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: m 110 LYS cc_start: 0.8407 (mtmm) cc_final: 0.7965 (mptp) REVERT: m 168 MET cc_start: 0.9253 (mmm) cc_final: 0.8977 (mmm) REVERT: m 216 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.9070 (t80) REVERT: h 43 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7388 (mm-30) REVERT: h 134 MET cc_start: 0.8105 (ttp) cc_final: 0.7573 (ttp) REVERT: a 30 MET cc_start: 0.8951 (ttt) cc_final: 0.8654 (ttt) REVERT: d 3 LYS cc_start: 0.8719 (mtpm) cc_final: 0.8463 (ttpt) REVERT: d 5 TYR cc_start: 0.8993 (p90) cc_final: 0.8402 (p90) REVERT: e 14 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8046 (t70) REVERT: e 15 GLU cc_start: 0.8060 (mp0) cc_final: 0.7843 (mp0) REVERT: f 6 LYS cc_start: 0.8736 (mttp) cc_final: 0.8394 (mttm) REVERT: f 9 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8788 (mmm) REVERT: f 15 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.6839 (mtm110) REVERT: i 3 LYS cc_start: 0.8829 (mttm) cc_final: 0.8364 (mtmt) REVERT: i 6 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8438 (mtmm) REVERT: i 9 MET cc_start: 0.8900 (mtm) cc_final: 0.8670 (mtm) REVERT: n 14 ASP cc_start: 0.7878 (t70) cc_final: 0.7413 (t0) REVERT: n 20 LEU cc_start: 0.8963 (tp) cc_final: 0.8644 (tm) REVERT: o 9 MET cc_start: 0.8491 (mmm) cc_final: 0.7952 (mmt) REVERT: o 11 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: p 16 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7468 (pm20) REVERT: r 18 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: t 42 VAL cc_start: 0.9144 (t) cc_final: 0.8906 (t) REVERT: v 25 MET cc_start: 0.8333 (mmm) cc_final: 0.7778 (mmm) REVERT: w 15 ARG cc_start: 0.5122 (OUTLIER) cc_final: 0.4214 (mtp180) REVERT: w 38 THR cc_start: 0.7376 (p) cc_final: 0.7146 (t) REVERT: 5 9 MET cc_start: 0.4091 (mmm) cc_final: 0.3768 (mmm) REVERT: z 25 MET cc_start: 0.6211 (mmm) cc_final: 0.5950 (mmm) REVERT: x 8 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7929 (p0) REVERT: x 66 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7731 (p0) outliers start: 77 outliers final: 48 residues processed: 717 average time/residue: 0.4265 time to fit residues: 387.4548 Evaluate side-chains 741 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 671 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain 3 residue 45 GLU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 100 GLU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 16 GLN Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 15 ARG Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain x residue 8 ASN Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 329 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 420 optimal weight: 0.0050 chunk 130 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 326 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN O 20 GLN R 16 GLN T 16 GLN 8 18 GLN 9 52 ASN X 61 GLN X 66 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN n 16 GLN o 20 GLN r 16 GLN t 16 GLN b9 52 ASN x 61 GLN x 66 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.149136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109777 restraints weight = 54227.417| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.35 r_work: 0.2862 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 46764 Z= 0.141 Angle : 0.633 14.813 64156 Z= 0.264 Chirality : 0.037 0.137 6242 Planarity : 0.003 0.038 7898 Dihedral : 15.519 122.505 8434 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.02 % Allowed : 15.36 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.65 (0.12), residues: 4482 helix: 2.50 (0.09), residues: 2982 sheet: -0.57 (0.76), residues: 48 loop : 0.31 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG l 135 TYR 0.021 0.001 TYR f 5 PHE 0.018 0.001 PHE h 20 TRP 0.018 0.001 TRP 5 8 HIS 0.009 0.001 HIS l 190 Details of bonding type rmsd covalent geometry : bond 0.00321 (46700) covalent geometry : angle 0.63347 (64156) hydrogen bonds : bond 0.04575 ( 2642) hydrogen bonds : angle 3.75501 ( 7458) Misc. bond : bond 0.00248 ( 64) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11136.78 seconds wall clock time: 189 minutes 55.38 seconds (11395.38 seconds total)