Starting phenix.real_space_refine on Wed Aug 27 02:15:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygd_39244/08_2025/8ygd_39244.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygd_39244/08_2025/8ygd_39244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygd_39244/08_2025/8ygd_39244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygd_39244/08_2025/8ygd_39244.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygd_39244/08_2025/8ygd_39244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygd_39244/08_2025/8ygd_39244.cif" } resolution = 2.84 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= 0.005 sd= 0.082 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 34 5.49 5 Mg 68 5.21 5 S 132 5.16 5 C 32920 2.51 5 N 6378 2.21 5 O 6976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 46510 Number of models: 1 Model: "" Number of chains: 134 Chain: "0" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "1" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "2" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 319 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "3" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "7" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 379 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "8" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "9" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "A" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "B" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "D" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "E" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "H" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1980 Classifications: {'peptide': 254} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 235} Chain: "I" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "J" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "L" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain: "M" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2432 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "N" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "P" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "R" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "T" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "U" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "V" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 432 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "X" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 451 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "Z" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 338 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "a" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "b" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 300 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "0" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 117 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'SPO': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'SPO:plan-4': 1} Unresolved non-hydrogen planarities: 3 Chain: "9" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 289 Unusual residues: {'BCL': 2, 'CDL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 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: 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: "L" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 539 Unusual residues: {'BCL': 3, 'BPH': 2, 'PC1': 1, 'U10': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'U10:plan-8': 4, 'U10:plan-9': 5, 'U10:plan-10': 5, 'U10:plan-11': 5, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 2} Unresolved non-hydrogen planarities: 100 Chain: "M" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 487 Unusual residues: {'BCL': 1, 'CDL': 2, 'FE2': 1, 'PC1': 4, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" 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: "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: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "X" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'U10': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "Z" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "a" 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: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "4" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "5" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 319 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "6" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "c" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 379 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "d" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "e" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "f" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "h" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "i" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "j" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "k" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "l" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "m" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1980 Classifications: {'peptide': 254} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 235} Chain: "n" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "o" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "p" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "q" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain: "r" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2432 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "s" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "t" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "u" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "v" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "w" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "x" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "y" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "z" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "AA" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "AB" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 432 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "AC" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 451 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "AD" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 338 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "AE" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "AF" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 300 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "Y" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "4" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 117 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'SPO': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'SPO:plan-4': 1} Unresolved non-hydrogen planarities: 3 Chain: "e" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "f" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "g" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "j" Number of atoms: 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: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 289 Unusual residues: {'BCL': 2, 'CDL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "m" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 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: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 539 Unusual residues: {'BCL': 3, 'BPH': 2, 'PC1': 1, 'U10': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'U10:plan-8': 4, 'U10:plan-9': 5, 'U10:plan-10': 5, 'U10:plan-11': 5, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 2} Unresolved non-hydrogen planarities: 100 Chain: "r" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 487 Unusual residues: {'BCL': 1, 'CDL': 2, 'FE2': 1, 'PC1': 4, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "s" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "v" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "w" 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: "x" 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: "y" 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: "z" 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: "AA" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "AC" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'U10': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "AD" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "AE" 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: "AF" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.65, per 1000 atoms: 0.25 Number of scatterers: 46510 At special positions: 0 Unit cell: (170.007, 222.031, 98.474, 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 132 16.00 P 34 15.00 Mg 68 11.99 O 6976 8.00 N 6378 7.00 C 32920 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=22, symmetry=0 Number of additional bonds: simple=22, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.08 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.7 microseconds 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8532 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 14 sheets defined 74.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain '0' and resid 13 through 46 Processing helix chain '1' and resid 5 through 11 removed outlier: 4.056A pdb=" N GLN 1 9 " --> pdb=" O TYR 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 38 removed outlier: 3.849A pdb=" N LYS 1 38 " --> pdb=" O ILE 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 51 Processing helix chain '2' and resid 13 through 46 removed outlier: 3.758A pdb=" N LEU 2 30 " --> pdb=" O SER 2 26 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 11 Processing helix chain '3' and resid 12 through 38 removed outlier: 3.568A pdb=" N VAL 3 16 " --> pdb=" O ASP 3 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL 3 18 " --> pdb=" O ARG 3 14 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 51 Processing helix chain '7' and resid 3 through 10 Processing helix chain '7' and resid 12 through 38 removed outlier: 3.760A pdb=" N LYS 7 38 " --> pdb=" O ILE 7 34 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 46 Processing helix chain '9' and resid 3 through 10 Processing helix chain '9' and resid 12 through 38 removed outlier: 3.762A pdb=" N LYS 9 38 " --> pdb=" O ILE 9 34 " (cutoff:3.500A) Processing helix chain '9' and resid 42 through 51 Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'B' and resid 13 through 46 Processing helix chain 'C' and resid 20 through 51 Processing helix chain 'D' and resid 3 through 5 No H-bonds generated for 'chain 'D' and resid 3 through 5' Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 37 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: 4.305A pdb=" N TYR F 5 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 7 " --> pdb=" O PHE F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 38 removed outlier: 3.676A pdb=" N LYS F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 52 Processing helix chain 'G' and resid 13 through 46 Processing helix chain 'H' and resid 11 through 35 Processing helix chain 'H' and resid 67 through 70 removed outlier: 3.578A pdb=" N ARG H 70 " --> pdb=" O PRO H 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 67 through 70' Processing helix chain 'H' and resid 77 through 84 removed outlier: 3.589A pdb=" N GLU H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 113 through 117 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 230 through 243 Processing helix chain 'H' and resid 243 through 248 Processing helix chain 'I' and resid 3 through 5 No H-bonds generated for 'chain 'I' and resid 3 through 5' Processing helix chain 'I' and resid 6 through 11 Processing helix chain 'I' and resid 12 through 38 removed outlier: 3.712A pdb=" N LYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 41 No H-bonds generated for 'chain 'I' and resid 39 through 41' Processing helix chain 'I' and resid 42 through 51 Processing helix chain 'J' and resid 13 through 46 removed outlier: 3.611A pdb=" N GLU J 19 " --> pdb=" O GLU J 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 5 No H-bonds generated for 'chain 'K' and resid 3 through 5' Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 12 through 38 Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'L' and resid 33 through 58 Processing helix chain 'L' and resid 80 through 83 Processing helix chain 'L' and resid 84 through 112 Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.659A pdb=" N PHE L 120 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'L' and resid 142 through 146 Processing helix chain 'L' and resid 153 through 164 Processing helix chain 'L' and resid 165 through 166 No H-bonds generated for 'chain 'L' and resid 165 through 166' Processing helix chain 'L' and resid 167 through 170 Processing helix chain 'L' and resid 171 through 200 Processing helix chain 'L' and resid 209 through 222 Processing helix chain 'L' and resid 226 through 251 removed outlier: 4.102A pdb=" N HIS L 231 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE L 251 " --> pdb=" O VAL L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 263 removed outlier: 3.569A pdb=" N ASN L 262 " --> pdb=" O GLN L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 3.983A pdb=" N VAL L 268 " --> pdb=" O TRP L 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 30 Processing helix chain 'M' and resid 37 through 42 removed outlier: 3.617A pdb=" N GLY M 41 " --> pdb=" O TRP M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 82 through 90 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 109 through 140 removed outlier: 3.550A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.658A pdb=" N SER M 152 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.646A pdb=" N GLU M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 234 through 240 removed outlier: 3.776A pdb=" N VAL M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 263 through 290 removed outlier: 3.618A pdb=" N TRP M 271 " --> pdb=" O ARG M 267 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL M 274 " --> pdb=" O TRP M 270 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL M 276 " --> pdb=" O PHE M 272 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR M 277 " --> pdb=" O GLY M 273 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY M 280 " --> pdb=" O VAL M 276 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER M 287 " --> pdb=" O GLY M 283 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLY M 288 " --> pdb=" O ILE M 284 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR M 289 " --> pdb=" O LEU M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 302 removed outlier: 3.675A pdb=" N TRP M 297 " --> pdb=" O ASN M 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 46 Processing helix chain 'O' and resid 2 through 10 removed outlier: 4.563A pdb=" N TYR O 5 " --> pdb=" O SER O 2 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP O 8 " --> pdb=" O TYR O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 37 removed outlier: 3.510A pdb=" N VAL O 16 " --> pdb=" O ASP O 12 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 52 Processing helix chain 'P' and resid 13 through 46 Processing helix chain 'Q' and resid 3 through 10 removed outlier: 3.972A pdb=" N TRP Q 8 " --> pdb=" O TYR Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 37 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 5 No H-bonds generated for 'chain 'S' and resid 3 through 5' Processing helix chain 'S' and resid 6 through 11 Processing helix chain 'S' and resid 12 through 38 removed outlier: 3.633A pdb=" N VAL S 16 " --> pdb=" O ASP S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 52 Processing helix chain 'T' and resid 13 through 46 Processing helix chain 'U' and resid 3 through 10 removed outlier: 3.715A pdb=" N TRP U 8 " --> pdb=" O TYR U 5 " (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 5 No H-bonds generated for 'chain 'W' and resid 3 through 5' Processing helix chain 'W' and resid 6 through 11 removed outlier: 3.779A pdb=" N VAL W 10 " --> pdb=" O LYS W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 38 removed outlier: 3.959A pdb=" N VAL W 22 " --> pdb=" O VAL W 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS W 38 " --> pdb=" O ILE W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 51 Processing helix chain 'X' and resid 11 through 51 Processing helix chain 'X' and resid 52 through 59 removed outlier: 5.921A pdb=" N GLN X 55 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER X 56 " --> pdb=" O PRO X 53 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA X 59 " --> pdb=" O SER X 56 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 46 removed outlier: 4.708A pdb=" N GLN Z 16 " --> pdb=" O LEU Z 12 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN Z 18 " --> pdb=" O ASP Z 14 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU Z 19 " --> pdb=" O GLU Z 15 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 11 Processing helix chain 'a' and resid 12 through 38 removed outlier: 3.695A pdb=" N VAL a 16 " --> pdb=" O ASP a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 52 Processing helix chain 'b' and resid 14 through 46 removed outlier: 3.518A pdb=" N VAL b 23 " --> pdb=" O GLU b 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 46 Processing helix chain '4' and resid 5 through 11 removed outlier: 4.056A pdb=" N GLN 4 9 " --> pdb=" O TYR 4 5 " (cutoff:3.500A) Processing helix chain '4' and resid 12 through 38 removed outlier: 3.849A pdb=" N LYS 4 38 " --> pdb=" O ILE 4 34 " (cutoff:3.500A) Processing helix chain '4' and resid 42 through 51 Processing helix chain '5' and resid 13 through 46 removed outlier: 3.758A pdb=" N LEU 5 30 " --> pdb=" O SER 5 26 " (cutoff:3.500A) Processing helix chain '6' and resid 6 through 11 Processing helix chain '6' and resid 12 through 38 removed outlier: 3.568A pdb=" N VAL 6 16 " --> pdb=" O ASP 6 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL 6 18 " --> pdb=" O ARG 6 14 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 51 Processing helix chain 'c' and resid 3 through 10 Processing helix chain 'c' and resid 12 through 38 removed outlier: 3.760A pdb=" N LYS c 38 " --> pdb=" O ILE c 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 46 Processing helix chain 'e' and resid 3 through 10 Processing helix chain 'e' and resid 12 through 38 removed outlier: 3.762A pdb=" N LYS e 38 " --> pdb=" O ILE e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 51 Processing helix chain 'f' and resid 3 through 10 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 'h' and resid 20 through 51 Processing helix chain 'i' and resid 3 through 5 No H-bonds generated for 'chain 'i' and resid 3 through 5' Processing helix chain 'i' and resid 6 through 11 Processing helix chain 'i' and resid 12 through 37 Processing helix chain 'i' and resid 42 through 51 Processing helix chain 'j' and resid 13 through 46 Processing helix chain 'k' and resid 2 through 10 removed outlier: 4.305A pdb=" N TYR k 5 " --> pdb=" O SER k 2 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE k 7 " --> pdb=" O PHE k 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 38 removed outlier: 3.676A pdb=" N LYS k 38 " --> pdb=" O ILE k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 42 through 52 Processing helix chain 'l' and resid 13 through 46 Processing helix chain 'm' and resid 11 through 35 Processing helix chain 'm' and resid 67 through 70 removed outlier: 3.578A pdb=" N ARG m 70 " --> pdb=" O PRO m 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 67 through 70' Processing helix chain 'm' and resid 77 through 84 removed outlier: 3.589A pdb=" N GLU m 81 " --> pdb=" O SER m 77 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 112 Processing helix chain 'm' and resid 113 through 117 Processing helix chain 'm' and resid 198 through 200 No H-bonds generated for 'chain 'm' and resid 198 through 200' Processing helix chain 'm' and resid 230 through 243 Processing helix chain 'm' and resid 243 through 248 Processing helix chain 'n' and resid 3 through 5 No H-bonds generated for 'chain 'n' and resid 3 through 5' Processing helix chain 'n' and resid 6 through 11 Processing helix chain 'n' and resid 12 through 38 removed outlier: 3.712A pdb=" N LYS n 38 " --> pdb=" O ILE n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 39 through 41 No H-bonds generated for 'chain 'n' and resid 39 through 41' Processing helix chain 'n' and resid 42 through 51 Processing helix chain 'o' and resid 13 through 46 removed outlier: 3.611A pdb=" N GLU o 19 " --> pdb=" O GLU o 15 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 5 No H-bonds generated for 'chain 'p' and resid 3 through 5' Processing helix chain 'p' and resid 6 through 11 Processing helix chain 'p' and resid 12 through 38 Processing helix chain 'p' and resid 42 through 51 Processing helix chain 'q' and resid 33 through 58 Processing helix chain 'q' and resid 80 through 83 Processing helix chain 'q' and resid 84 through 112 Processing helix chain 'q' and resid 116 through 134 removed outlier: 3.659A pdb=" N PHE q 120 " --> pdb=" O LEU q 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE q 124 " --> pdb=" O PHE q 120 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA q 125 " --> pdb=" O ALA q 121 " (cutoff:3.500A) Processing helix chain 'q' and resid 134 through 141 Processing helix chain 'q' and resid 142 through 146 Processing helix chain 'q' and resid 153 through 164 Processing helix chain 'q' and resid 165 through 166 No H-bonds generated for 'chain 'q' and resid 165 through 166' Processing helix chain 'q' and resid 167 through 170 Processing helix chain 'q' and resid 171 through 200 Processing helix chain 'q' and resid 209 through 222 Processing helix chain 'q' and resid 226 through 251 removed outlier: 4.102A pdb=" N HIS q 231 " --> pdb=" O THR q 227 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE q 251 " --> pdb=" O VAL q 247 " (cutoff:3.500A) Processing helix chain 'q' and resid 259 through 263 removed outlier: 3.569A pdb=" N ASN q 262 " --> pdb=" O GLN q 259 " (cutoff:3.500A) Processing helix chain 'q' and resid 264 through 269 removed outlier: 3.983A pdb=" N VAL q 268 " --> pdb=" O TRP q 264 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 30 Processing helix chain 'r' and resid 37 through 42 removed outlier: 3.617A pdb=" N GLY r 41 " --> pdb=" O TRP r 37 " (cutoff:3.500A) Processing helix chain 'r' and resid 54 through 79 Processing helix chain 'r' and resid 82 through 90 Processing helix chain 'r' and resid 99 through 103 Processing helix chain 'r' and resid 109 through 140 removed outlier: 3.550A pdb=" N LEU r 140 " --> pdb=" O ARG r 136 " (cutoff:3.500A) Processing helix chain 'r' and resid 144 through 162 removed outlier: 3.658A pdb=" N SER r 152 " --> pdb=" O TRP r 148 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA r 153 " --> pdb=" O ALA r 149 " (cutoff:3.500A) Processing helix chain 'r' and resid 162 through 169 Processing helix chain 'r' and resid 170 through 174 removed outlier: 3.646A pdb=" N GLU r 173 " --> pdb=" O SER r 170 " (cutoff:3.500A) Processing helix chain 'r' and resid 180 through 193 Processing helix chain 'r' and resid 195 through 198 Processing helix chain 'r' and resid 199 through 226 Processing helix chain 'r' and resid 227 through 230 Processing helix chain 'r' and resid 234 through 240 removed outlier: 3.776A pdb=" N VAL r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) Processing helix chain 'r' and resid 242 through 257 Processing helix chain 'r' and resid 263 through 290 removed outlier: 3.618A pdb=" N TRP r 271 " --> pdb=" O ARG r 267 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL r 274 " --> pdb=" O TRP r 270 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL r 276 " --> pdb=" O PHE r 272 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR r 277 " --> pdb=" O GLY r 273 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY r 280 " --> pdb=" O VAL r 276 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER r 287 " --> pdb=" O GLY r 283 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLY r 288 " --> pdb=" O ILE r 284 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR r 289 " --> pdb=" O LEU r 285 " (cutoff:3.500A) Processing helix chain 'r' and resid 293 through 302 removed outlier: 3.675A pdb=" N TRP r 297 " --> pdb=" O ASN r 293 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 46 Processing helix chain 't' and resid 2 through 10 removed outlier: 4.563A pdb=" N TYR t 5 " --> pdb=" O SER t 2 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP t 8 " --> pdb=" O TYR t 5 " (cutoff:3.500A) Processing helix chain 't' and resid 12 through 37 removed outlier: 3.510A pdb=" N VAL t 16 " --> pdb=" O ASP t 12 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL t 18 " --> pdb=" O ARG t 14 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 52 Processing helix chain 'u' and resid 13 through 46 Processing helix chain 'v' and resid 3 through 10 removed outlier: 3.972A pdb=" N TRP v 8 " --> pdb=" O TYR v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 12 through 37 Processing helix chain 'v' and resid 42 through 51 Processing helix chain 'w' and resid 13 through 46 Processing helix chain 'x' and resid 3 through 5 No H-bonds generated for 'chain 'x' and resid 3 through 5' Processing helix chain 'x' and resid 6 through 11 Processing helix chain 'x' and resid 12 through 38 removed outlier: 3.633A pdb=" N VAL x 16 " --> pdb=" O ASP x 12 " (cutoff:3.500A) Processing helix chain 'x' and resid 42 through 52 Processing helix chain 'y' and resid 13 through 46 Processing helix chain 'z' and resid 3 through 10 removed outlier: 3.715A pdb=" N TRP z 8 " --> pdb=" O TYR z 5 " (cutoff:3.500A) Processing helix chain 'z' and resid 12 through 38 Processing helix chain 'z' and resid 42 through 51 Processing helix chain 'AA' and resid 13 through 46 Processing helix chain 'AB' and resid 3 through 5 No H-bonds generated for 'chain 'AB' and resid 3 through 5' Processing helix chain 'AB' and resid 6 through 11 removed outlier: 3.779A pdb=" N VALAB 10 " --> pdb=" O LYSAB 6 " (cutoff:3.500A) Processing helix chain 'AB' and resid 12 through 38 removed outlier: 3.959A pdb=" N VALAB 22 " --> pdb=" O VALAB 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYSAB 38 " --> pdb=" O ILEAB 34 " (cutoff:3.500A) Processing helix chain 'AB' and resid 42 through 51 Processing helix chain 'AC' and resid 11 through 51 Processing helix chain 'AC' and resid 52 through 59 removed outlier: 5.921A pdb=" N GLNAC 55 " --> pdb=" O LEUAC 52 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SERAC 56 " --> pdb=" O PROAC 53 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAAC 59 " --> pdb=" O SERAC 56 " (cutoff:3.500A) Processing helix chain 'AD' and resid 12 through 46 removed outlier: 4.708A pdb=" N GLNAD 16 " --> pdb=" O LEUAD 12 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLNAD 18 " --> pdb=" O ASPAD 14 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLUAD 19 " --> pdb=" O GLUAD 15 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRPAD 45 " --> pdb=" O ALAAD 41 " (cutoff:3.500A) Processing helix chain 'AE' and resid 6 through 11 Processing helix chain 'AE' and resid 12 through 38 removed outlier: 3.695A pdb=" N VALAE 16 " --> pdb=" O ASPAE 12 " (cutoff:3.500A) Processing helix chain 'AE' and resid 42 through 52 Processing helix chain 'AF' and resid 14 through 46 removed outlier: 3.518A pdb=" N VALAF 23 " --> pdb=" O GLUAF 19 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'H' and resid 62 through 65 Processing sheet with id=2, first strand: chain 'H' and resid 91 through 93 Processing sheet with id=3, first strand: chain 'H' and resid 135 through 137 removed outlier: 6.277A pdb=" N GLY H 166 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU H 187 " --> pdb=" O GLY H 166 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL H 168 " --> pdb=" O ILE H 185 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE H 185 " --> pdb=" O VAL H 168 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU H 170 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU H 183 " --> pdb=" O GLU H 170 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TRP H 172 " --> pdb=" O ARG H 181 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'H' and resid 135 through 137 removed outlier: 6.578A pdb=" N VAL H 164 " --> pdb=" O ALA H 159 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA H 159 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY H 166 " --> pdb=" O VAL H 157 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'H' and resid 145 through 149 removed outlier: 3.515A pdb=" N ASN H 145 " --> pdb=" O GLY M 14 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR H 147 " --> pdb=" O GLN M 12 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN M 12 " --> pdb=" O THR H 147 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'L' and resid 25 through 27 removed outlier: 4.127A pdb=" N PHE L 25 " --> pdb=" O VAL L 32 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'L' and resid 66 through 67 removed outlier: 3.553A pdb=" N ILE L 67 " --> pdb=" O TYR L 149 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'm' and resid 62 through 65 Processing sheet with id=9, first strand: chain 'm' and resid 91 through 93 Processing sheet with id=10, first strand: chain 'm' and resid 135 through 137 removed outlier: 6.277A pdb=" N GLY m 166 " --> pdb=" O LEU m 187 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU m 187 " --> pdb=" O GLY m 166 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL m 168 " --> pdb=" O ILE m 185 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE m 185 " --> pdb=" O VAL m 168 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU m 170 " --> pdb=" O LEU m 183 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU m 183 " --> pdb=" O GLU m 170 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TRP m 172 " --> pdb=" O ARG m 181 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'm' and resid 135 through 137 removed outlier: 6.578A pdb=" N VAL m 164 " --> pdb=" O ALA m 159 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA m 159 " --> pdb=" O VAL m 164 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY m 166 " --> pdb=" O VAL m 157 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'm' and resid 145 through 149 removed outlier: 3.515A pdb=" N ASN m 145 " --> pdb=" O GLY r 14 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR m 147 " --> pdb=" O GLN r 12 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN r 12 " --> pdb=" O THR m 147 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'q' and resid 25 through 27 removed outlier: 4.127A pdb=" N PHE q 25 " --> pdb=" O VAL q 32 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'q' and resid 66 through 67 removed outlier: 3.553A pdb=" N ILE q 67 " --> pdb=" O TYR q 149 " (cutoff:3.500A) 2584 hydrogen bonds defined for protein. 7434 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: 7.98 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 13286 1.36 - 1.54: 34200 1.54 - 1.73: 226 1.73 - 1.92: 256 1.92 - 2.10: 272 Bond restraints: 48240 Sorted by residual: bond pdb=" CB7 CDL F 101 " pdb=" OB8 CDL F 101 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" CB7 CDL k 101 " pdb=" OB8 CDL k 101 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" CA7 CDL k 101 " pdb=" OA8 CDL k 101 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CA7 CDL F 101 " pdb=" OA8 CDL F 101 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.18e+02 bond pdb=" NA BCL g 101 " pdb="MG BCL g 101 " ideal model delta sigma weight residual 2.170 1.979 0.191 2.40e-02 1.74e+03 6.31e+01 ... (remaining 48235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 61046 3.01 - 6.02: 4184 6.02 - 9.03: 762 9.03 - 12.04: 144 12.04 - 15.06: 14 Bond angle restraints: 66150 Sorted by residual: angle pdb=" N VAL r 175 " pdb=" CA VAL r 175 " pdb=" C VAL r 175 " ideal model delta sigma weight residual 108.63 119.12 -10.49 8.60e-01 1.35e+00 1.49e+02 angle pdb=" N VAL M 175 " pdb=" CA VAL M 175 " pdb=" C VAL M 175 " ideal model delta sigma weight residual 108.63 119.12 -10.49 8.60e-01 1.35e+00 1.49e+02 angle pdb=" N ALA Z 17 " pdb=" CA ALA Z 17 " pdb=" C ALA Z 17 " ideal model delta sigma weight residual 111.28 102.38 8.90 1.09e+00 8.42e-01 6.66e+01 angle pdb=" N ALAAD 17 " pdb=" CA ALAAD 17 " pdb=" C ALAAD 17 " ideal model delta sigma weight residual 111.28 102.38 8.90 1.09e+00 8.42e-01 6.66e+01 angle pdb=" N PHE q 30 " pdb=" CA PHE q 30 " pdb=" C PHE q 30 " ideal model delta sigma weight residual 110.28 121.76 -11.48 1.48e+00 4.57e-01 6.01e+01 ... (remaining 66145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 24292 35.20 - 70.39: 1472 70.39 - 105.59: 96 105.59 - 140.78: 26 140.78 - 175.98: 24 Dihedral angle restraints: 25910 sinusoidal: 12632 harmonic: 13278 Sorted by residual: dihedral pdb=" C1 BCL J 102 " pdb=" CGA BCL J 102 " pdb=" O2A BCL J 102 " pdb=" CBA BCL J 102 " ideal model delta sinusoidal sigma weight residual -180.00 -13.03 -166.97 1 6.00e+00 2.78e-02 5.26e+02 dihedral pdb=" C1 BCL o 102 " pdb=" CGA BCL o 102 " pdb=" O2A BCL o 102 " pdb=" CBA BCL o 102 " ideal model delta sinusoidal sigma weight residual -180.00 -13.03 -166.97 1 6.00e+00 2.78e-02 5.26e+02 dihedral pdb=" C1 BCL 1 102 " pdb=" CGA BCL 1 102 " pdb=" O2A BCL 1 102 " pdb=" CBA BCL 1 102 " ideal model delta sinusoidal sigma weight residual -180.00 -43.84 -136.16 1 6.00e+00 2.78e-02 4.59e+02 ... (remaining 25907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.045: 6332 1.045 - 2.091: 0 2.091 - 3.136: 0 3.136 - 4.182: 0 4.182 - 5.227: 12 Chirality restraints: 6344 Sorted by residual: chirality pdb=" C18 BCL E 101 " pdb=" C17 BCL E 101 " pdb=" C19 BCL E 101 " pdb=" C20 BCL E 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.52 5.23 2.00e-01 2.50e+01 6.83e+02 chirality pdb=" C18 BCL j 101 " pdb=" C17 BCL j 101 " pdb=" C19 BCL j 101 " pdb=" C20 BCL j 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.52 5.23 2.00e-01 2.50e+01 6.83e+02 chirality pdb=" C18 BCL R 103 " pdb=" C17 BCL R 103 " pdb=" C19 BCL R 103 " pdb=" C20 BCL R 103 " both_signs ideal model delta sigma weight residual False 2.71 -2.50 5.21 2.00e-01 2.50e+01 6.78e+02 ... (remaining 6341 not shown) Planarity restraints: 8082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 6 102 " -0.365 1.50e-02 4.44e+03 3.07e-01 2.10e+03 pdb=" C2 BCL 6 102 " 0.534 1.50e-02 4.44e+03 pdb=" C3 BCL 6 102 " 0.113 1.50e-02 4.44e+03 pdb=" C4 BCL 6 102 " -0.120 1.50e-02 4.44e+03 pdb=" C5 BCL 6 102 " -0.163 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 3 102 " 0.365 1.50e-02 4.44e+03 3.07e-01 2.10e+03 pdb=" C2 BCL 3 102 " -0.534 1.50e-02 4.44e+03 pdb=" C3 BCL 3 102 " -0.113 1.50e-02 4.44e+03 pdb=" C4 BCL 3 102 " 0.120 1.50e-02 4.44e+03 pdb=" C5 BCL 3 102 " 0.163 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL E 101 " -0.363 1.50e-02 4.44e+03 3.06e-01 2.09e+03 pdb=" C2 BCL E 101 " 0.533 1.50e-02 4.44e+03 pdb=" C3 BCL E 101 " 0.113 1.50e-02 4.44e+03 pdb=" C4 BCL E 101 " -0.123 1.50e-02 4.44e+03 pdb=" C5 BCL E 101 " -0.159 1.50e-02 4.44e+03 ... (remaining 8079 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 8 2.18 - 2.86: 15336 2.86 - 3.54: 64675 3.54 - 4.22: 116113 4.22 - 4.90: 204680 Nonbonded interactions: 400812 Sorted by model distance: nonbonded pdb=" O LEU 7 44 " pdb=" NE1 TRP d 45 " model vdw 1.497 3.120 nonbonded pdb=" NE1 TRP 8 45 " pdb=" O LEU c 44 " model vdw 1.497 3.120 nonbonded pdb=" C14 BCL 7 101 " pdb=" C26 U10AC 101 " model vdw 1.691 3.088 nonbonded pdb=" C26 U10 X 101 " pdb=" C14 BCL c 101 " model vdw 1.691 3.088 nonbonded pdb=" C LEU 7 44 " pdb=" NE1 TRP d 45 " model vdw 2.080 3.350 ... (remaining 400807 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: 0.01 Found NCS groups: ncs_group { reference = (chain '0' and resid 10 through 48) selection = (chain '2' and resid 10 through 48) selection = (chain '5' and resid 10 through 48) selection = (chain '8' and resid 10 through 48) selection = (chain 'AA' and resid 10 through 48) selection = (chain 'AD' and resid 10 through 48) selection = (chain 'B' and resid 10 through 48) selection = (chain 'C' and resid 15 through 53) selection = (chain 'E' and resid 10 through 48) selection = (chain 'G' and resid 10 through 48) selection = (chain 'J' and resid 10 through 48) selection = (chain 'N' and resid 10 through 48) selection = (chain 'P' and resid 10 through 48) selection = (chain 'R' and resid 10 through 48) selection = (chain 'T' and resid 10 through 48) selection = (chain 'V' and resid 10 through 48) selection = (chain 'Y' and resid 10 through 48) selection = (chain 'Z' and resid 10 through 48) selection = (chain 'd' and resid 10 through 48) selection = (chain 'g' and resid 10 through 48) selection = (chain 'h' and resid 15 through 53) selection = (chain 'j' and resid 10 through 48) selection = (chain 'l' and resid 10 through 48) selection = (chain 'o' and resid 10 through 48) selection = (chain 's' and resid 10 through 48) selection = (chain 'u' and resid 10 through 48) selection = (chain 'w' and resid 10 through 48) selection = (chain 'y' and resid 10 through 48) } ncs_group { reference = (chain '1' and resid 5 through 52) selection = (chain '3' and resid 5 through 52) selection = (chain '4' and resid 5 through 52) selection = (chain '6' and resid 5 through 52) selection = (chain '9' and resid 5 through 52) selection = (chain 'A' and resid 5 through 52) selection = (chain 'AB' and resid 5 through 52) selection = (chain 'AE' and resid 5 through 52) selection = (chain 'D' and resid 5 through 52) selection = (chain 'F' and resid 5 through 52) selection = (chain 'I' and resid 5 through 52) selection = (chain 'K' and resid 5 through 52) selection = (chain 'O' and resid 5 through 52) selection = (chain 'Q' and resid 5 through 52) selection = (chain 'S' and resid 5 through 52) selection = (chain 'U' and resid 5 through 52) selection = (chain 'W' and resid 5 through 52) selection = (chain 'a' and resid 5 through 52) selection = (chain 'e' and resid 5 through 52) selection = (chain 'f' and resid 5 through 52) selection = (chain 'i' and resid 5 through 52) selection = (chain 'k' and resid 5 through 52) selection = (chain 'n' and resid 5 through 52) selection = (chain 'p' and resid 5 through 52) selection = (chain 't' and resid 5 through 52) selection = (chain 'v' and resid 5 through 52) selection = (chain 'x' and resid 5 through 52) selection = (chain 'z' and resid 5 through 52) } ncs_group { reference = chain '7' selection = chain 'c' } ncs_group { reference = chain 'AC' selection = chain 'X' } ncs_group { reference = chain 'AF' selection = chain 'b' } ncs_group { reference = chain 'H' selection = chain 'm' } ncs_group { reference = chain 'L' selection = chain 'q' } ncs_group { reference = chain 'M' selection = chain 'r' } 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: 1.580 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: 0.070 Extract box with map and model: 0.710 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 42.130 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.150 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:8.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.022 0.696 48262 Z= 1.521 Angle : 1.687 15.055 66150 Z= 0.879 Chirality : 0.250 5.227 6344 Planarity : 0.031 0.324 8082 Dihedral : 20.882 175.980 17378 Min Nonbonded Distance : 1.497 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.60 % Allowed : 6.08 % Favored : 92.32 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.11), residues: 4466 helix: -0.73 (0.09), residues: 3054 sheet: -2.01 (0.57), residues: 60 loop : -2.11 (0.15), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 136 TYR 0.032 0.002 TYR r 303 PHE 0.060 0.002 PHE r 216 TRP 0.051 0.002 TRP q 273 HIS 0.011 0.002 HIS r 182 Details of bonding type rmsd covalent geometry : bond 0.01869 (48240) covalent geometry : angle 1.68715 (66150) hydrogen bonds : bond 0.14161 ( 2580) hydrogen bonds : angle 5.79997 ( 7434) Misc. bond : bond 0.56895 ( 22) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 810 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 9 GLN cc_start: 0.6361 (mt0) cc_final: 0.6118 (mt0) REVERT: 1 24 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6389 (pp) REVERT: 2 19 GLU cc_start: 0.6891 (tt0) cc_final: 0.6555 (mt-10) REVERT: 9 3 LYS cc_start: 0.7883 (mttp) cc_final: 0.7580 (mtmm) REVERT: C 28 VAL cc_start: 0.8235 (m) cc_final: 0.7962 (t) REVERT: C 30 MET cc_start: 0.8535 (mmm) cc_final: 0.8159 (mpp) REVERT: C 34 TRP cc_start: 0.7377 (m100) cc_final: 0.7117 (t60) REVERT: G 8 SER cc_start: 0.8801 (p) cc_final: 0.8561 (p) REVERT: H 9 ASP cc_start: 0.7915 (m-30) cc_final: 0.7299 (p0) REVERT: H 36 MET cc_start: 0.7961 (mtt) cc_final: 0.7168 (mtm) REVERT: H 40 TYR cc_start: 0.8920 (m-80) cc_final: 0.8717 (m-80) REVERT: H 75 MET cc_start: 0.8619 (mtp) cc_final: 0.8269 (mtm) REVERT: H 170 GLU cc_start: 0.8039 (tp30) cc_final: 0.7833 (tp30) REVERT: I 11 PHE cc_start: 0.7890 (m-80) cc_final: 0.7553 (m-10) REVERT: J 22 SER cc_start: 0.8016 (t) cc_final: 0.7647 (p) REVERT: M 92 TYR cc_start: 0.8996 (m-80) cc_final: 0.8769 (m-80) REVERT: P 45 TRP cc_start: 0.8592 (t60) cc_final: 0.8382 (t60) REVERT: Q 3 LYS cc_start: 0.7413 (mtpt) cc_final: 0.6818 (mptm) REVERT: Q 12 ASP cc_start: 0.8068 (t70) cc_final: 0.7733 (t0) REVERT: S 9 GLN cc_start: 0.6327 (mt0) cc_final: 0.6032 (tt0) REVERT: S 38 LYS cc_start: 0.7639 (mmtm) cc_final: 0.7271 (mmtm) REVERT: S 40 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.6701 (p0) REVERT: S 41 TYR cc_start: 0.8349 (m-80) cc_final: 0.7410 (m-80) REVERT: S 43 TRP cc_start: 0.8298 (p90) cc_final: 0.8095 (p90) REVERT: U 12 ASP cc_start: 0.7817 (t0) cc_final: 0.7207 (t0) REVERT: U 14 ARG cc_start: 0.6562 (ttt180) cc_final: 0.5775 (mtm110) REVERT: V 43 TYR cc_start: 0.8204 (t80) cc_final: 0.7793 (t80) REVERT: V 49 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7605 (pt) REVERT: W 4 PHE cc_start: 0.7409 (m-80) cc_final: 0.7139 (m-80) REVERT: W 16 VAL cc_start: 0.8553 (p) cc_final: 0.8307 (p) REVERT: W 42 ASN cc_start: 0.8684 (t0) cc_final: 0.8369 (t0) REVERT: Z 20 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7232 (tt) REVERT: Z 21 HIS cc_start: 0.7463 (t70) cc_final: 0.7172 (t-90) REVERT: a 14 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6808 (mpp80) REVERT: a 27 LEU cc_start: 0.6809 (tp) cc_final: 0.6528 (mt) REVERT: a 36 LEU cc_start: 0.7996 (tp) cc_final: 0.7554 (mt) REVERT: a 42 ASN cc_start: 0.7417 (t0) cc_final: 0.7048 (t0) REVERT: 4 9 GLN cc_start: 0.6361 (mt0) cc_final: 0.6115 (mt0) REVERT: 4 24 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6388 (pp) REVERT: 5 19 GLU cc_start: 0.6891 (tt0) cc_final: 0.6556 (mt-10) REVERT: e 3 LYS cc_start: 0.7884 (mttp) cc_final: 0.7581 (mtmm) REVERT: h 28 VAL cc_start: 0.8235 (m) cc_final: 0.7961 (t) REVERT: h 30 MET cc_start: 0.8534 (mmm) cc_final: 0.8160 (mpp) REVERT: h 34 TRP cc_start: 0.7376 (m100) cc_final: 0.7116 (t60) REVERT: l 8 SER cc_start: 0.8801 (p) cc_final: 0.8561 (p) REVERT: m 9 ASP cc_start: 0.7916 (m-30) cc_final: 0.7300 (p0) REVERT: m 36 MET cc_start: 0.7960 (mtt) cc_final: 0.7167 (mtm) REVERT: m 40 TYR cc_start: 0.8920 (m-80) cc_final: 0.8716 (m-80) REVERT: m 75 MET cc_start: 0.8618 (mtp) cc_final: 0.8269 (mtm) REVERT: m 170 GLU cc_start: 0.8038 (tp30) cc_final: 0.7833 (tp30) REVERT: n 11 PHE cc_start: 0.7892 (m-80) cc_final: 0.7553 (m-10) REVERT: o 22 SER cc_start: 0.8019 (t) cc_final: 0.7650 (p) REVERT: r 92 TYR cc_start: 0.8997 (m-80) cc_final: 0.8770 (m-80) REVERT: u 45 TRP cc_start: 0.8592 (t60) cc_final: 0.8382 (t60) REVERT: v 3 LYS cc_start: 0.7413 (mtpt) cc_final: 0.6818 (mptm) REVERT: v 12 ASP cc_start: 0.8068 (t70) cc_final: 0.7732 (t0) REVERT: x 9 GLN cc_start: 0.6328 (mt0) cc_final: 0.6032 (tt0) REVERT: x 38 LYS cc_start: 0.7639 (mmtm) cc_final: 0.7272 (mmtm) REVERT: x 40 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.6697 (p0) REVERT: x 41 TYR cc_start: 0.8347 (m-80) cc_final: 0.7411 (m-80) REVERT: x 43 TRP cc_start: 0.8300 (p90) cc_final: 0.8097 (p90) REVERT: z 12 ASP cc_start: 0.7818 (t0) cc_final: 0.7209 (t0) REVERT: z 14 ARG cc_start: 0.6561 (ttt180) cc_final: 0.5775 (mtm110) REVERT: AA 43 TYR cc_start: 0.8204 (t80) cc_final: 0.7793 (t80) REVERT: AA 49 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7604 (pt) REVERT: AB 4 PHE cc_start: 0.7410 (m-80) cc_final: 0.7140 (m-80) REVERT: AB 16 VAL cc_start: 0.8553 (p) cc_final: 0.8307 (p) REVERT: AB 42 ASN cc_start: 0.8684 (t0) cc_final: 0.8370 (t0) REVERT: AD 20 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7232 (tt) REVERT: AD 21 HIS cc_start: 0.7464 (t70) cc_final: 0.7173 (t-90) REVERT: AE 14 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6808 (mpp80) REVERT: AE 27 LEU cc_start: 0.6808 (tp) cc_final: 0.6527 (mt) REVERT: AE 36 LEU cc_start: 0.7996 (tp) cc_final: 0.7554 (mt) REVERT: AE 42 ASN cc_start: 0.7417 (t0) cc_final: 0.7047 (t0) outliers start: 62 outliers final: 20 residues processed: 854 average time/residue: 0.5870 time to fit residues: 652.1529 Evaluate side-chains 650 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 622 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 31 PHE Chi-restraints excluded: chain 4 residue 24 LEU Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain h residue 54 LEU Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain q residue 248 CYS Chi-restraints excluded: chain x residue 40 ASP Chi-restraints excluded: chain AA residue 49 LEU Chi-restraints excluded: chain AB residue 7 ILE Chi-restraints excluded: chain AD residue 20 LEU Chi-restraints excluded: chain AE residue 16 VAL Chi-restraints excluded: chain AF residue 28 LEU Chi-restraints excluded: chain AF residue 31 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 9 GLN 2 18 GLN 2 21 HIS 2 39 HIS 7 9 GLN 9 9 GLN C 23 GLN F 20 GLN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 HIS I 9 GLN M 36 ASN M 45 ASN O 32 HIS P 16 GLN U 20 GLN ** U 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 GLN ** W 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 16 GLN 4 9 GLN 5 18 GLN 5 21 HIS 5 39 HIS c 9 GLN e 9 GLN h 23 GLN k 20 GLN m 130 HIS n 9 GLN r 36 ASN r 45 ASN t 32 HIS u 16 GLN z 20 GLN ** z 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 18 GLN ** AB 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 16 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.158737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.126006 restraints weight = 65286.105| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.88 r_work: 0.3414 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 48262 Z= 0.178 Angle : 0.905 18.582 66150 Z= 0.349 Chirality : 0.041 0.209 6344 Planarity : 0.004 0.047 8082 Dihedral : 20.257 179.813 9262 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.47 % Allowed : 13.04 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: 0.61 (0.12), residues: 4466 helix: 1.10 (0.09), residues: 3056 sheet: -1.28 (0.78), residues: 40 loop : -1.07 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 85 TYR 0.021 0.001 TYR M 303 PHE 0.013 0.001 PHE L 23 TRP 0.023 0.002 TRP M 37 HIS 0.008 0.001 HIS 5 39 Details of bonding type rmsd covalent geometry : bond 0.00428 (48240) covalent geometry : angle 0.90495 (66150) hydrogen bonds : bond 0.05250 ( 2580) hydrogen bonds : angle 4.15593 ( 7434) Misc. bond : bond 0.00161 ( 22) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 706 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 40 ASP cc_start: 0.7775 (m-30) cc_final: 0.7278 (t0) REVERT: 2 19 GLU cc_start: 0.6509 (tt0) cc_final: 0.6152 (mt-10) REVERT: 3 4 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6932 (m-80) REVERT: 8 44 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8217 (mp) REVERT: 9 3 LYS cc_start: 0.7661 (mttp) cc_final: 0.7137 (mtmm) REVERT: C 30 MET cc_start: 0.8517 (mmm) cc_final: 0.8032 (mpp) REVERT: C 34 TRP cc_start: 0.7586 (m100) cc_final: 0.7006 (t60) REVERT: D 51 TYR cc_start: 0.8824 (m-80) cc_final: 0.8553 (m-10) REVERT: G 8 SER cc_start: 0.8777 (p) cc_final: 0.8170 (t) REVERT: H 9 ASP cc_start: 0.8170 (m-30) cc_final: 0.7216 (p0) REVERT: H 170 GLU cc_start: 0.8493 (tp30) cc_final: 0.7990 (tp30) REVERT: H 219 ASN cc_start: 0.8895 (m-40) cc_final: 0.8665 (m-40) REVERT: I 11 PHE cc_start: 0.7663 (m-80) cc_final: 0.7257 (m-10) REVERT: I 30 MET cc_start: 0.8440 (ttp) cc_final: 0.8128 (ttt) REVERT: J 18 GLN cc_start: 0.7421 (mt0) cc_final: 0.7214 (mt0) REVERT: J 22 SER cc_start: 0.8129 (t) cc_final: 0.7626 (p) REVERT: J 25 MET cc_start: 0.8355 (mmm) cc_final: 0.8109 (mmm) REVERT: L 214 ASP cc_start: 0.8701 (m-30) cc_final: 0.8439 (m-30) REVERT: L 248 CYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8184 (p) REVERT: M 32 LYS cc_start: 0.8432 (mmtm) cc_final: 0.8226 (mmtm) REVERT: N 43 TYR cc_start: 0.8163 (t80) cc_final: 0.7931 (t80) REVERT: Q 3 LYS cc_start: 0.7312 (mtpt) cc_final: 0.6630 (mptm) REVERT: S 9 GLN cc_start: 0.6169 (mt0) cc_final: 0.5775 (tt0) REVERT: V 49 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7431 (pt) REVERT: W 4 PHE cc_start: 0.7287 (m-80) cc_final: 0.6874 (m-80) REVERT: a 14 ARG cc_start: 0.6998 (mtt180) cc_final: 0.6720 (mpp80) REVERT: a 36 LEU cc_start: 0.7532 (tp) cc_final: 0.7142 (mt) REVERT: a 40 ASP cc_start: 0.6174 (t0) cc_final: 0.5959 (t0) REVERT: 4 40 ASP cc_start: 0.7759 (m-30) cc_final: 0.7273 (t0) REVERT: 5 19 GLU cc_start: 0.6513 (tt0) cc_final: 0.6146 (mt-10) REVERT: 6 4 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: d 44 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8217 (mp) REVERT: e 3 LYS cc_start: 0.7670 (mttp) cc_final: 0.7143 (mtmm) REVERT: h 30 MET cc_start: 0.8514 (mmm) cc_final: 0.8026 (mpp) REVERT: h 34 TRP cc_start: 0.7577 (m100) cc_final: 0.7004 (t60) REVERT: i 51 TYR cc_start: 0.8828 (m-80) cc_final: 0.8565 (m-10) REVERT: l 8 SER cc_start: 0.8788 (p) cc_final: 0.8180 (t) REVERT: m 9 ASP cc_start: 0.8174 (m-30) cc_final: 0.7215 (p0) REVERT: m 170 GLU cc_start: 0.8497 (tp30) cc_final: 0.7998 (tp30) REVERT: m 219 ASN cc_start: 0.8886 (m-40) cc_final: 0.8658 (m-40) REVERT: n 11 PHE cc_start: 0.7654 (m-80) cc_final: 0.7252 (m-10) REVERT: n 30 MET cc_start: 0.8446 (ttp) cc_final: 0.8126 (ttt) REVERT: o 18 GLN cc_start: 0.7421 (mt0) cc_final: 0.7217 (mt0) REVERT: o 22 SER cc_start: 0.8119 (t) cc_final: 0.7619 (p) REVERT: o 25 MET cc_start: 0.8352 (mmm) cc_final: 0.8104 (mmm) REVERT: q 214 ASP cc_start: 0.8714 (m-30) cc_final: 0.8460 (m-30) REVERT: q 248 CYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8192 (p) REVERT: r 32 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8213 (mmtm) REVERT: s 43 TYR cc_start: 0.8173 (t80) cc_final: 0.7934 (t80) REVERT: v 3 LYS cc_start: 0.7308 (mtpt) cc_final: 0.6638 (mptm) REVERT: x 9 GLN cc_start: 0.6176 (mt0) cc_final: 0.5782 (tt0) REVERT: AA 49 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7420 (pt) REVERT: AB 4 PHE cc_start: 0.7278 (m-80) cc_final: 0.6869 (m-80) REVERT: AE 14 ARG cc_start: 0.6936 (mtt180) cc_final: 0.6664 (mpp80) REVERT: AE 36 LEU cc_start: 0.7536 (tp) cc_final: 0.7148 (mt) REVERT: AE 40 ASP cc_start: 0.6165 (t0) cc_final: 0.5965 (t0) outliers start: 96 outliers final: 26 residues processed: 756 average time/residue: 0.5823 time to fit residues: 580.3010 Evaluate side-chains 658 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 624 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 4 PHE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 8 residue 44 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain 6 residue 4 PHE Chi-restraints excluded: chain 6 residue 33 LEU Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 248 CYS Chi-restraints excluded: chain r residue 306 VAL Chi-restraints excluded: chain s residue 10 THR Chi-restraints excluded: chain t residue 2 SER Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain x residue 16 VAL Chi-restraints excluded: chain AA residue 49 LEU Chi-restraints excluded: chain AB residue 36 LEU Chi-restraints excluded: chain AC residue 33 VAL Chi-restraints excluded: chain AD residue 15 GLU Chi-restraints excluded: chain AE residue 16 VAL Chi-restraints excluded: chain AE residue 45 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 414 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 404 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 424 optimal weight: 4.9990 chunk 15 optimal weight: 30.0000 chunk 123 optimal weight: 4.9990 chunk 400 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 311 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 9 GLN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN M 10 GLN M 29 ASN M 45 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN S 42 ASN ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 9 GLN ** k 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 10 GLN r 29 ASN r 45 ASN ** r 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN x 42 ASN ** AD 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 32 HIS ** AF 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.152306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118415 restraints weight = 66633.349| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.05 r_work: 0.3290 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 48262 Z= 0.245 Angle : 0.904 16.788 66150 Z= 0.359 Chirality : 0.043 0.189 6344 Planarity : 0.004 0.049 8082 Dihedral : 19.490 179.625 9222 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.61 % Allowed : 15.80 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: 0.97 (0.12), residues: 4466 helix: 1.32 (0.09), residues: 3080 sheet: -1.54 (0.71), residues: 40 loop : -0.80 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 46 TYR 0.018 0.002 TYR r 303 PHE 0.017 0.002 PHE S 11 TRP 0.019 0.002 TRP V 48 HIS 0.009 0.002 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00594 (48240) covalent geometry : angle 0.90368 (66150) hydrogen bonds : bond 0.05283 ( 2580) hydrogen bonds : angle 4.09202 ( 7434) Misc. bond : bond 0.00253 ( 22) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 740 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 30 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7531 (ttt) REVERT: 1 40 ASP cc_start: 0.7972 (m-30) cc_final: 0.7463 (t0) REVERT: 2 19 GLU cc_start: 0.6587 (tt0) cc_final: 0.6247 (mt-10) REVERT: 8 44 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8230 (mp) REVERT: 9 3 LYS cc_start: 0.7565 (mttp) cc_final: 0.7103 (mtmm) REVERT: B 18 GLN cc_start: 0.7538 (tt0) cc_final: 0.7186 (tp-100) REVERT: C 30 MET cc_start: 0.8547 (mmm) cc_final: 0.8044 (mpp) REVERT: C 34 TRP cc_start: 0.7683 (m100) cc_final: 0.7035 (t60) REVERT: C 53 TRP cc_start: 0.6604 (p90) cc_final: 0.6391 (p90) REVERT: D 29 VAL cc_start: 0.9022 (t) cc_final: 0.8719 (m) REVERT: F 42 ASN cc_start: 0.8913 (t0) cc_final: 0.8350 (t0) REVERT: G 8 SER cc_start: 0.8776 (p) cc_final: 0.8123 (t) REVERT: G 12 LEU cc_start: 0.8001 (mt) cc_final: 0.7736 (tp) REVERT: H 44 MET cc_start: 0.8293 (mmm) cc_final: 0.7999 (mmm) REVERT: I 10 VAL cc_start: 0.7265 (t) cc_final: 0.7055 (t) REVERT: I 11 PHE cc_start: 0.7591 (m-80) cc_final: 0.6907 (m-10) REVERT: J 15 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6788 (pm20) REVERT: J 25 MET cc_start: 0.8355 (mmm) cc_final: 0.8020 (mmm) REVERT: L 202 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7722 (mt-10) REVERT: L 214 ASP cc_start: 0.8701 (m-30) cc_final: 0.8390 (m-30) REVERT: L 240 MET cc_start: 0.8399 (mmm) cc_final: 0.8029 (mmp) REVERT: L 269 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7217 (mm-30) REVERT: M 40 LEU cc_start: 0.8548 (mt) cc_final: 0.8344 (mt) REVERT: M 101 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8269 (ptmt) REVERT: M 108 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7987 (mtt180) REVERT: N 43 TYR cc_start: 0.8159 (t80) cc_final: 0.7858 (t80) REVERT: Q 3 LYS cc_start: 0.7277 (mtpt) cc_final: 0.6561 (mptm) REVERT: Q 12 ASP cc_start: 0.7639 (t70) cc_final: 0.7369 (t0) REVERT: S 9 GLN cc_start: 0.6297 (mt0) cc_final: 0.5849 (tt0) REVERT: S 12 ASP cc_start: 0.7853 (t70) cc_final: 0.7456 (t70) REVERT: U 14 ARG cc_start: 0.6475 (ttt180) cc_final: 0.5440 (mtm110) REVERT: U 42 ASN cc_start: 0.8278 (t0) cc_final: 0.7616 (t0) REVERT: V 18 GLN cc_start: 0.7847 (tp40) cc_final: 0.7603 (mm110) REVERT: V 49 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7273 (pt) REVERT: W 4 PHE cc_start: 0.7189 (m-80) cc_final: 0.6708 (m-80) REVERT: W 8 TRP cc_start: 0.7494 (m100) cc_final: 0.6956 (m100) REVERT: W 31 ILE cc_start: 0.8138 (mt) cc_final: 0.7897 (mp) REVERT: W 42 ASN cc_start: 0.8301 (t0) cc_final: 0.7731 (t0) REVERT: a 14 ARG cc_start: 0.6827 (mtt180) cc_final: 0.6509 (mpp80) REVERT: a 36 LEU cc_start: 0.7314 (tp) cc_final: 0.6845 (mt) REVERT: 4 30 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7548 (ttt) REVERT: 4 40 ASP cc_start: 0.7966 (m-30) cc_final: 0.7455 (t0) REVERT: 5 19 GLU cc_start: 0.6590 (tt0) cc_final: 0.6249 (mt-10) REVERT: d 44 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8232 (mp) REVERT: e 3 LYS cc_start: 0.7572 (mttp) cc_final: 0.7101 (mtmm) REVERT: g 18 GLN cc_start: 0.7552 (tt0) cc_final: 0.7201 (tp-100) REVERT: h 30 MET cc_start: 0.8551 (mmm) cc_final: 0.8044 (mpp) REVERT: h 34 TRP cc_start: 0.7683 (m100) cc_final: 0.7034 (t60) REVERT: h 53 TRP cc_start: 0.6595 (p90) cc_final: 0.6383 (p90) REVERT: i 29 VAL cc_start: 0.9013 (t) cc_final: 0.8716 (m) REVERT: k 42 ASN cc_start: 0.8914 (t0) cc_final: 0.8356 (t0) REVERT: l 8 SER cc_start: 0.8771 (p) cc_final: 0.8113 (t) REVERT: l 12 LEU cc_start: 0.7980 (mt) cc_final: 0.7713 (tp) REVERT: m 44 MET cc_start: 0.8301 (mmm) cc_final: 0.8010 (mmm) REVERT: n 10 VAL cc_start: 0.7256 (t) cc_final: 0.7050 (t) REVERT: n 11 PHE cc_start: 0.7580 (m-80) cc_final: 0.6908 (m-10) REVERT: o 15 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6810 (pm20) REVERT: o 25 MET cc_start: 0.8360 (mmm) cc_final: 0.8022 (mmm) REVERT: q 202 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7708 (mt-10) REVERT: q 214 ASP cc_start: 0.8707 (m-30) cc_final: 0.8404 (m-30) REVERT: q 240 MET cc_start: 0.8393 (mmm) cc_final: 0.8020 (mmp) REVERT: q 269 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7226 (mm-30) REVERT: r 32 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8076 (mmtm) REVERT: r 40 LEU cc_start: 0.8540 (mt) cc_final: 0.8333 (mt) REVERT: r 101 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8294 (ptmt) REVERT: r 108 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7992 (mtt180) REVERT: s 43 TYR cc_start: 0.8162 (t80) cc_final: 0.7858 (t80) REVERT: v 3 LYS cc_start: 0.7271 (mtpt) cc_final: 0.6561 (mptm) REVERT: v 12 ASP cc_start: 0.7635 (t70) cc_final: 0.7368 (t0) REVERT: x 9 GLN cc_start: 0.6302 (mt0) cc_final: 0.5853 (tt0) REVERT: x 12 ASP cc_start: 0.7858 (t70) cc_final: 0.7464 (t70) REVERT: z 14 ARG cc_start: 0.6468 (ttt180) cc_final: 0.5437 (mtm110) REVERT: z 42 ASN cc_start: 0.8276 (t0) cc_final: 0.7616 (t0) REVERT: AA 18 GLN cc_start: 0.7843 (tp40) cc_final: 0.7598 (mm110) REVERT: AA 49 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7279 (pt) REVERT: AB 4 PHE cc_start: 0.7204 (m-80) cc_final: 0.6727 (m-80) REVERT: AB 8 TRP cc_start: 0.7492 (m100) cc_final: 0.6956 (m100) REVERT: AB 31 ILE cc_start: 0.8137 (mt) cc_final: 0.7899 (mp) REVERT: AB 42 ASN cc_start: 0.8283 (t0) cc_final: 0.7717 (t0) REVERT: AE 14 ARG cc_start: 0.6849 (mtt180) cc_final: 0.6528 (mpp80) REVERT: AE 36 LEU cc_start: 0.7316 (tp) cc_final: 0.6845 (mt) outliers start: 140 outliers final: 46 residues processed: 808 average time/residue: 0.5706 time to fit residues: 609.9649 Evaluate side-chains 704 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 646 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 44 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain V residue 25 MET Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 41 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain 4 residue 30 MET Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain m residue 150 ARG Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain o residue 15 GLU Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain r residue 29 ASN Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 108 ARG Chi-restraints excluded: chain r residue 306 VAL Chi-restraints excluded: chain s residue 10 THR Chi-restraints excluded: chain t residue 2 SER Chi-restraints excluded: chain u residue 15 GLU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain x residue 16 VAL Chi-restraints excluded: chain x residue 37 SER Chi-restraints excluded: chain AA residue 25 MET Chi-restraints excluded: chain AA residue 49 LEU Chi-restraints excluded: chain AB residue 36 LEU Chi-restraints excluded: chain AC residue 33 VAL Chi-restraints excluded: chain AC residue 41 LEU Chi-restraints excluded: chain AD residue 15 GLU Chi-restraints excluded: chain AE residue 16 VAL Chi-restraints excluded: chain AE residue 45 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 374 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 387 optimal weight: 8.9990 chunk 332 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 21 HIS ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN M 29 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 21 HIS Q 20 GLN a 32 HIS 5 21 HIS ** l 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 10 GLN r 29 ASN ** r 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 21 HIS v 20 GLN AC 5 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.157434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120908 restraints weight = 65929.733| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.62 r_work: 0.3395 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 48262 Z= 0.124 Angle : 0.776 13.709 66150 Z= 0.302 Chirality : 0.038 0.217 6344 Planarity : 0.003 0.043 8082 Dihedral : 18.646 179.875 9220 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.60 % Allowed : 17.53 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.12), residues: 4466 helix: 1.82 (0.09), residues: 3068 sheet: -1.44 (0.69), residues: 40 loop : -0.50 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAB 15 TYR 0.016 0.001 TYR r 303 PHE 0.012 0.001 PHE L 147 TRP 0.019 0.001 TRP M 74 HIS 0.012 0.001 HIS P 21 Details of bonding type rmsd covalent geometry : bond 0.00283 (48240) covalent geometry : angle 0.77576 (66150) hydrogen bonds : bond 0.04547 ( 2580) hydrogen bonds : angle 3.82295 ( 7434) Misc. bond : bond 0.00124 ( 22) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 730 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 25 MET cc_start: 0.8490 (mmm) cc_final: 0.8275 (mmp) REVERT: 1 30 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7462 (ttm) REVERT: 1 40 ASP cc_start: 0.8027 (m-30) cc_final: 0.7515 (t0) REVERT: 2 19 GLU cc_start: 0.6547 (tt0) cc_final: 0.6275 (mt-10) REVERT: 3 4 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.7016 (m-80) REVERT: 8 25 MET cc_start: 0.7896 (mmt) cc_final: 0.7645 (mmp) REVERT: 8 44 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8142 (mp) REVERT: 9 3 LYS cc_start: 0.7256 (mttp) cc_final: 0.6692 (mppt) REVERT: 9 12 ASP cc_start: 0.8880 (t70) cc_final: 0.8538 (t70) REVERT: A 34 ILE cc_start: 0.8753 (mt) cc_final: 0.8457 (mm) REVERT: B 18 GLN cc_start: 0.7313 (tt0) cc_final: 0.6937 (tp-100) REVERT: C 12 LEU cc_start: 0.1289 (OUTLIER) cc_final: 0.0680 (pp) REVERT: C 30 MET cc_start: 0.8415 (mmm) cc_final: 0.7867 (mpp) REVERT: C 34 TRP cc_start: 0.7675 (m100) cc_final: 0.7027 (t60) REVERT: D 29 VAL cc_start: 0.8784 (t) cc_final: 0.8460 (m) REVERT: D 40 ASP cc_start: 0.8066 (t70) cc_final: 0.7586 (t0) REVERT: G 8 SER cc_start: 0.8643 (p) cc_final: 0.7938 (t) REVERT: H 44 MET cc_start: 0.8135 (mmm) cc_final: 0.7746 (mmm) REVERT: H 98 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8076 (mm-30) REVERT: H 136 MET cc_start: 0.7596 (mtm) cc_final: 0.6885 (ptp) REVERT: H 150 ARG cc_start: 0.6106 (mpt180) cc_final: 0.5532 (mmt180) REVERT: I 9 GLN cc_start: 0.7594 (mt0) cc_final: 0.6995 (mt0) REVERT: I 30 MET cc_start: 0.8075 (ttp) cc_final: 0.7744 (ttt) REVERT: I 41 TYR cc_start: 0.9108 (m-80) cc_final: 0.8900 (m-80) REVERT: J 22 SER cc_start: 0.7989 (t) cc_final: 0.7506 (p) REVERT: J 25 MET cc_start: 0.8189 (mmm) cc_final: 0.7823 (mmm) REVERT: K 6 LYS cc_start: 0.7576 (mmtt) cc_final: 0.6746 (mmmt) REVERT: K 9 GLN cc_start: 0.7675 (mt0) cc_final: 0.7400 (mt0) REVERT: L 202 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7538 (mt-10) REVERT: L 214 ASP cc_start: 0.8445 (m-30) cc_final: 0.8179 (m-30) REVERT: L 240 MET cc_start: 0.8072 (mmm) cc_final: 0.7703 (mmp) REVERT: L 255 ILE cc_start: 0.8695 (mt) cc_final: 0.8365 (mm) REVERT: L 269 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7226 (mm-30) REVERT: M 19 MET cc_start: 0.7481 (mmp) cc_final: 0.7125 (mmm) REVERT: M 108 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7838 (mtt180) REVERT: N 43 TYR cc_start: 0.8072 (t80) cc_final: 0.7862 (t80) REVERT: O 8 TRP cc_start: 0.8357 (m100) cc_final: 0.7937 (m100) REVERT: Q 3 LYS cc_start: 0.7181 (mtpt) cc_final: 0.6545 (mptm) REVERT: R 21 HIS cc_start: 0.7438 (t-170) cc_final: 0.7025 (t-90) REVERT: R 33 THR cc_start: 0.9061 (p) cc_final: 0.8835 (t) REVERT: S 9 GLN cc_start: 0.6340 (mt0) cc_final: 0.5846 (tt0) REVERT: U 30 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7273 (mtm) REVERT: U 42 ASN cc_start: 0.8023 (t0) cc_final: 0.7402 (t0) REVERT: V 18 GLN cc_start: 0.7768 (tp40) cc_final: 0.7562 (mm110) REVERT: W 4 PHE cc_start: 0.7067 (m-80) cc_final: 0.6387 (m-80) REVERT: W 7 ILE cc_start: 0.8572 (tt) cc_final: 0.8051 (pt) REVERT: Z 15 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6704 (pm20) REVERT: Z 21 HIS cc_start: 0.7236 (t-90) cc_final: 0.7003 (t70) REVERT: Z 25 MET cc_start: 0.6890 (ptt) cc_final: 0.6317 (ppp) REVERT: a 14 ARG cc_start: 0.6613 (mtt180) cc_final: 0.6304 (mpp80) REVERT: a 36 LEU cc_start: 0.7254 (tp) cc_final: 0.6813 (mt) REVERT: Y 25 MET cc_start: 0.8479 (mmm) cc_final: 0.8261 (mmp) REVERT: 4 30 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7448 (ttm) REVERT: 4 40 ASP cc_start: 0.8019 (m-30) cc_final: 0.7512 (t0) REVERT: 5 19 GLU cc_start: 0.6546 (tt0) cc_final: 0.6275 (mt-10) REVERT: 6 4 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.7018 (m-80) REVERT: d 25 MET cc_start: 0.7894 (mmt) cc_final: 0.7644 (mmp) REVERT: d 44 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8143 (mp) REVERT: e 3 LYS cc_start: 0.7281 (mttp) cc_final: 0.6700 (mppt) REVERT: e 12 ASP cc_start: 0.8868 (t70) cc_final: 0.8524 (t70) REVERT: f 34 ILE cc_start: 0.8770 (mt) cc_final: 0.8474 (mm) REVERT: g 18 GLN cc_start: 0.7323 (tt0) cc_final: 0.6953 (tp-100) REVERT: h 12 LEU cc_start: 0.1290 (OUTLIER) cc_final: 0.0681 (pp) REVERT: h 30 MET cc_start: 0.8419 (mmm) cc_final: 0.7866 (mpp) REVERT: h 34 TRP cc_start: 0.7674 (m100) cc_final: 0.7028 (t60) REVERT: i 29 VAL cc_start: 0.8783 (t) cc_final: 0.8460 (m) REVERT: i 40 ASP cc_start: 0.8075 (t70) cc_final: 0.7585 (t0) REVERT: l 8 SER cc_start: 0.8647 (p) cc_final: 0.7937 (t) REVERT: m 44 MET cc_start: 0.8128 (mmm) cc_final: 0.7738 (mmm) REVERT: m 98 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8074 (mm-30) REVERT: m 136 MET cc_start: 0.7596 (mtm) cc_final: 0.6896 (ptp) REVERT: m 150 ARG cc_start: 0.6100 (mpt180) cc_final: 0.5527 (mmt180) REVERT: n 9 GLN cc_start: 0.7601 (mt0) cc_final: 0.6996 (mt0) REVERT: n 30 MET cc_start: 0.8068 (ttp) cc_final: 0.7744 (ttt) REVERT: n 41 TYR cc_start: 0.9112 (m-80) cc_final: 0.8902 (m-80) REVERT: o 22 SER cc_start: 0.7987 (t) cc_final: 0.7503 (p) REVERT: o 25 MET cc_start: 0.8177 (mmm) cc_final: 0.7810 (mmm) REVERT: p 6 LYS cc_start: 0.7574 (mmtt) cc_final: 0.6750 (mmmt) REVERT: p 9 GLN cc_start: 0.7676 (mt0) cc_final: 0.7411 (mt0) REVERT: q 202 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7519 (mt-10) REVERT: q 214 ASP cc_start: 0.8440 (m-30) cc_final: 0.8197 (m-30) REVERT: q 240 MET cc_start: 0.8071 (mmm) cc_final: 0.7702 (mmp) REVERT: q 255 ILE cc_start: 0.8698 (mt) cc_final: 0.8371 (mm) REVERT: q 269 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7240 (mm-30) REVERT: r 19 MET cc_start: 0.7464 (mmp) cc_final: 0.7111 (mmm) REVERT: r 108 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7860 (mtt180) REVERT: s 43 TYR cc_start: 0.8086 (t80) cc_final: 0.7871 (t80) REVERT: t 8 TRP cc_start: 0.8365 (m100) cc_final: 0.7946 (m100) REVERT: v 3 LYS cc_start: 0.7179 (mtpt) cc_final: 0.6546 (mptm) REVERT: w 21 HIS cc_start: 0.7436 (t-170) cc_final: 0.7025 (t-90) REVERT: w 33 THR cc_start: 0.9064 (p) cc_final: 0.8834 (t) REVERT: x 9 GLN cc_start: 0.6339 (mt0) cc_final: 0.5846 (tt0) REVERT: z 30 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7276 (mtm) REVERT: z 42 ASN cc_start: 0.8023 (t0) cc_final: 0.7399 (t0) REVERT: AA 18 GLN cc_start: 0.7767 (tp40) cc_final: 0.7562 (mm110) REVERT: AB 4 PHE cc_start: 0.7053 (m-80) cc_final: 0.6376 (m-80) REVERT: AB 7 ILE cc_start: 0.8574 (tt) cc_final: 0.8052 (pt) REVERT: AD 15 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6706 (pm20) REVERT: AD 21 HIS cc_start: 0.7242 (t-90) cc_final: 0.7009 (t70) REVERT: AD 25 MET cc_start: 0.6898 (ptt) cc_final: 0.6324 (ppp) REVERT: AE 14 ARG cc_start: 0.6621 (mtt180) cc_final: 0.6318 (mpp80) REVERT: AE 36 LEU cc_start: 0.7255 (tp) cc_final: 0.6813 (mt) outliers start: 101 outliers final: 29 residues processed: 775 average time/residue: 0.5366 time to fit residues: 552.9623 Evaluate side-chains 697 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 654 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 3 residue 4 PHE Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 44 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 128 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain X residue 16 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain 4 residue 30 MET Chi-restraints excluded: chain 6 residue 4 PHE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain r residue 108 ARG Chi-restraints excluded: chain r residue 128 SER Chi-restraints excluded: chain s residue 10 THR Chi-restraints excluded: chain t residue 2 SER Chi-restraints excluded: chain u residue 15 GLU Chi-restraints excluded: chain x residue 16 VAL Chi-restraints excluded: chain z residue 30 MET Chi-restraints excluded: chain AB residue 36 LEU Chi-restraints excluded: chain AC residue 5 ASN Chi-restraints excluded: chain AC residue 16 LEU Chi-restraints excluded: chain AD residue 15 GLU Chi-restraints excluded: chain AE residue 16 VAL Chi-restraints excluded: chain AE residue 45 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 26 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 423 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 422 optimal weight: 3.9990 chunk 410 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 421 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 21 HIS ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN M 29 ASN M 45 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN S 42 ASN ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 21 HIS ** l 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 10 GLN r 29 ASN r 45 ASN ** r 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN x 42 ASN ** AF 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.118781 restraints weight = 66037.844| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.54 r_work: 0.3355 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 48262 Z= 0.166 Angle : 0.802 13.699 66150 Z= 0.316 Chirality : 0.039 0.221 6344 Planarity : 0.004 0.044 8082 Dihedral : 18.479 179.924 9216 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.63 % Allowed : 19.12 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.12), residues: 4466 helix: 1.82 (0.09), residues: 3078 sheet: -1.40 (0.69), residues: 40 loop : -0.40 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 3 53 TYR 0.015 0.001 TYR r 303 PHE 0.035 0.001 PHE 3 25 TRP 0.017 0.001 TRP M 74 HIS 0.010 0.001 HIS P 21 Details of bonding type rmsd covalent geometry : bond 0.00396 (48240) covalent geometry : angle 0.80160 (66150) hydrogen bonds : bond 0.04685 ( 2580) hydrogen bonds : angle 3.84918 ( 7434) Misc. bond : bond 0.00169 ( 22) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 706 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 30 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7490 (ttm) REVERT: 1 40 ASP cc_start: 0.8052 (m-30) cc_final: 0.7568 (t0) REVERT: 2 19 GLU cc_start: 0.6609 (tt0) cc_final: 0.6324 (mt-10) REVERT: 3 4 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6011 (t80) REVERT: 8 25 MET cc_start: 0.8067 (mmt) cc_final: 0.7799 (mmp) REVERT: 8 44 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8185 (mp) REVERT: 9 3 LYS cc_start: 0.7429 (mttp) cc_final: 0.6864 (mppt) REVERT: 9 12 ASP cc_start: 0.8950 (t70) cc_final: 0.8630 (t70) REVERT: A 34 ILE cc_start: 0.8904 (mt) cc_final: 0.8622 (mm) REVERT: B 18 GLN cc_start: 0.7474 (tt0) cc_final: 0.7122 (tp-100) REVERT: C 12 LEU cc_start: 0.1292 (OUTLIER) cc_final: 0.0728 (pp) REVERT: C 30 MET cc_start: 0.8456 (mmm) cc_final: 0.7922 (mpp) REVERT: C 34 TRP cc_start: 0.7691 (m100) cc_final: 0.7053 (t60) REVERT: C 53 TRP cc_start: 0.6449 (p90) cc_final: 0.6227 (p90) REVERT: D 29 VAL cc_start: 0.8961 (t) cc_final: 0.8629 (m) REVERT: D 40 ASP cc_start: 0.8149 (t70) cc_final: 0.7647 (t0) REVERT: G 8 SER cc_start: 0.8734 (p) cc_final: 0.8049 (t) REVERT: H 38 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: H 44 MET cc_start: 0.8196 (mmm) cc_final: 0.7770 (mmm) REVERT: H 98 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8087 (mm-30) REVERT: H 174 ASP cc_start: 0.8862 (t0) cc_final: 0.8587 (t0) REVERT: I 9 GLN cc_start: 0.7704 (mt0) cc_final: 0.7064 (mt0) REVERT: J 25 MET cc_start: 0.8309 (mmm) cc_final: 0.7934 (mmm) REVERT: L 240 MET cc_start: 0.8221 (mmm) cc_final: 0.7856 (mmp) REVERT: L 255 ILE cc_start: 0.8688 (mt) cc_final: 0.8412 (mm) REVERT: L 269 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7316 (mm-30) REVERT: M 19 MET cc_start: 0.7558 (mmp) cc_final: 0.7148 (mmm) REVERT: M 108 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7972 (mtt180) REVERT: O 8 TRP cc_start: 0.8503 (m100) cc_final: 0.8115 (m100) REVERT: Q 3 LYS cc_start: 0.7246 (mtpt) cc_final: 0.6571 (mptm) REVERT: R 33 THR cc_start: 0.9060 (p) cc_final: 0.8851 (t) REVERT: S 9 GLN cc_start: 0.6328 (mt0) cc_final: 0.5952 (tt0) REVERT: U 30 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7308 (mtm) REVERT: U 42 ASN cc_start: 0.8131 (t0) cc_final: 0.7427 (t0) REVERT: V 49 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6868 (pt) REVERT: W 4 PHE cc_start: 0.7172 (m-80) cc_final: 0.6509 (m-80) REVERT: W 7 ILE cc_start: 0.8622 (tt) cc_final: 0.8123 (pt) REVERT: W 15 ARG cc_start: 0.5308 (ttm170) cc_final: 0.4141 (tmt-80) REVERT: W 33 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8292 (mp) REVERT: W 42 ASN cc_start: 0.8123 (t0) cc_final: 0.7508 (t0) REVERT: Z 15 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6678 (pm20) REVERT: Z 21 HIS cc_start: 0.7341 (t-90) cc_final: 0.6939 (t70) REVERT: Z 25 MET cc_start: 0.6900 (ptt) cc_final: 0.6327 (ppp) REVERT: a 36 LEU cc_start: 0.7324 (tp) cc_final: 0.6872 (mt) REVERT: 4 30 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7497 (ttm) REVERT: 4 40 ASP cc_start: 0.8047 (m-30) cc_final: 0.7567 (t0) REVERT: 5 19 GLU cc_start: 0.6609 (tt0) cc_final: 0.6331 (mt-10) REVERT: 6 4 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.5996 (t80) REVERT: d 25 MET cc_start: 0.8066 (mmt) cc_final: 0.7799 (mmp) REVERT: d 44 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8189 (mp) REVERT: e 3 LYS cc_start: 0.7444 (mttp) cc_final: 0.6878 (mppt) REVERT: e 12 ASP cc_start: 0.8943 (t70) cc_final: 0.8624 (t70) REVERT: f 34 ILE cc_start: 0.8920 (mt) cc_final: 0.8639 (mm) REVERT: g 18 GLN cc_start: 0.7476 (tt0) cc_final: 0.7130 (tp-100) REVERT: h 12 LEU cc_start: 0.1294 (OUTLIER) cc_final: 0.0729 (pp) REVERT: h 30 MET cc_start: 0.8459 (mmm) cc_final: 0.7926 (mpp) REVERT: h 34 TRP cc_start: 0.7688 (m100) cc_final: 0.7054 (t60) REVERT: h 53 TRP cc_start: 0.6455 (p90) cc_final: 0.6235 (p90) REVERT: i 29 VAL cc_start: 0.8946 (t) cc_final: 0.8614 (m) REVERT: i 40 ASP cc_start: 0.8156 (t70) cc_final: 0.7646 (t0) REVERT: l 8 SER cc_start: 0.8725 (p) cc_final: 0.8034 (t) REVERT: m 38 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: m 44 MET cc_start: 0.8199 (mmm) cc_final: 0.7771 (mmm) REVERT: m 98 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8091 (mm-30) REVERT: m 174 ASP cc_start: 0.8861 (t0) cc_final: 0.8594 (t0) REVERT: n 9 GLN cc_start: 0.7706 (mt0) cc_final: 0.7061 (mt0) REVERT: o 25 MET cc_start: 0.8300 (mmm) cc_final: 0.7925 (mmm) REVERT: q 240 MET cc_start: 0.8228 (mmm) cc_final: 0.7860 (mmp) REVERT: q 255 ILE cc_start: 0.8683 (mt) cc_final: 0.8411 (mm) REVERT: q 269 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7332 (mm-30) REVERT: r 19 MET cc_start: 0.7555 (mmp) cc_final: 0.7144 (mmm) REVERT: r 108 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7977 (mtt180) REVERT: t 8 TRP cc_start: 0.8502 (m100) cc_final: 0.8114 (m100) REVERT: v 3 LYS cc_start: 0.7252 (mtpt) cc_final: 0.6578 (mptm) REVERT: w 33 THR cc_start: 0.9059 (p) cc_final: 0.8849 (t) REVERT: x 9 GLN cc_start: 0.6336 (mt0) cc_final: 0.5960 (tt0) REVERT: z 30 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7321 (mtm) REVERT: z 42 ASN cc_start: 0.8137 (t0) cc_final: 0.7431 (t0) REVERT: AA 49 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.6858 (pt) REVERT: AB 4 PHE cc_start: 0.7163 (m-80) cc_final: 0.6502 (m-80) REVERT: AB 7 ILE cc_start: 0.8622 (tt) cc_final: 0.8121 (pt) REVERT: AB 15 ARG cc_start: 0.5316 (ttm170) cc_final: 0.4153 (tmt-80) REVERT: AB 33 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8285 (mp) REVERT: AB 42 ASN cc_start: 0.8118 (t0) cc_final: 0.7504 (t0) REVERT: AD 15 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6679 (pm20) REVERT: AD 21 HIS cc_start: 0.7346 (t-90) cc_final: 0.6943 (t70) REVERT: AD 25 MET cc_start: 0.6907 (ptt) cc_final: 0.6332 (ppp) REVERT: AE 36 LEU cc_start: 0.7328 (tp) cc_final: 0.6875 (mt) outliers start: 102 outliers final: 40 residues processed: 762 average time/residue: 0.3861 time to fit residues: 392.0787 Evaluate side-chains 722 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 662 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 3 residue 4 PHE Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 44 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 128 SER Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain T residue 21 HIS Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 30 MET Chi-restraints excluded: chain 6 residue 4 PHE Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain m residue 38 GLU Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain o residue 20 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain r residue 29 ASN Chi-restraints excluded: chain r residue 108 ARG Chi-restraints excluded: chain r residue 128 SER Chi-restraints excluded: chain r residue 306 VAL Chi-restraints excluded: chain s residue 10 THR Chi-restraints excluded: chain t residue 2 SER Chi-restraints excluded: chain w residue 12 LEU Chi-restraints excluded: chain x residue 16 VAL Chi-restraints excluded: chain y residue 21 HIS Chi-restraints excluded: chain z residue 30 MET Chi-restraints excluded: chain AA residue 49 LEU Chi-restraints excluded: chain AB residue 33 LEU Chi-restraints excluded: chain AB residue 36 LEU Chi-restraints excluded: chain AD residue 15 GLU Chi-restraints excluded: chain AE residue 16 VAL Chi-restraints excluded: chain AE residue 45 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 354 optimal weight: 5.9990 chunk 436 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 349 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 357 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 401 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 21 HIS D 20 GLN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN M 29 ASN M 45 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN b 39 HIS 5 21 HIS i 20 GLN ** k 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 10 GLN r 29 ASN ** r 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN AF 39 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.153022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119432 restraints weight = 66542.551| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.53 r_work: 0.3349 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 48262 Z= 0.208 Angle : 0.833 13.716 66150 Z= 0.332 Chirality : 0.041 0.227 6344 Planarity : 0.004 0.043 8082 Dihedral : 18.606 179.921 9216 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.71 % Allowed : 20.08 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.12), residues: 4466 helix: 1.68 (0.09), residues: 3086 sheet: -1.48 (0.69), residues: 40 loop : -0.41 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 6 53 TYR 0.016 0.002 TYR M 303 PHE 0.035 0.002 PHE 3 25 TRP 0.032 0.002 TRP L 272 HIS 0.008 0.001 HIS r 182 Details of bonding type rmsd covalent geometry : bond 0.00505 (48240) covalent geometry : angle 0.83254 (66150) hydrogen bonds : bond 0.04948 ( 2580) hydrogen bonds : angle 3.94001 ( 7434) Misc. bond : bond 0.00191 ( 22) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 688 time to evaluate : 0.927 Fit side-chains REVERT: 1 30 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7583 (ttm) REVERT: 1 40 ASP cc_start: 0.7934 (m-30) cc_final: 0.7376 (t0) REVERT: 2 19 GLU cc_start: 0.6619 (tt0) cc_final: 0.6335 (mt-10) REVERT: 3 42 ASN cc_start: 0.6676 (t0) cc_final: 0.6423 (t0) REVERT: 8 44 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8277 (mp) REVERT: 9 3 LYS cc_start: 0.7628 (mttp) cc_final: 0.7041 (mppt) REVERT: 9 12 ASP cc_start: 0.9002 (t70) cc_final: 0.8757 (t70) REVERT: B 18 GLN cc_start: 0.7515 (tt0) cc_final: 0.7273 (tp-100) REVERT: C 12 LEU cc_start: 0.1548 (OUTLIER) cc_final: 0.0849 (pp) REVERT: C 30 MET cc_start: 0.8512 (mmm) cc_final: 0.7900 (mpp) REVERT: C 34 TRP cc_start: 0.7654 (m100) cc_final: 0.7080 (t60) REVERT: C 53 TRP cc_start: 0.6466 (p90) cc_final: 0.6241 (p90) REVERT: D 29 VAL cc_start: 0.9101 (t) cc_final: 0.8750 (m) REVERT: D 40 ASP cc_start: 0.8161 (t70) cc_final: 0.7718 (t0) REVERT: G 8 SER cc_start: 0.8828 (p) cc_final: 0.8179 (t) REVERT: G 15 GLU cc_start: 0.8640 (pm20) cc_final: 0.7991 (mm-30) REVERT: H 44 MET cc_start: 0.8324 (mmm) cc_final: 0.7901 (mmm) REVERT: H 98 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8106 (mm-30) REVERT: H 136 MET cc_start: 0.7957 (mtm) cc_final: 0.7555 (ptp) REVERT: I 9 GLN cc_start: 0.7787 (mt0) cc_final: 0.7120 (mt0) REVERT: J 25 MET cc_start: 0.8505 (mmm) cc_final: 0.8235 (mmm) REVERT: K 17 PHE cc_start: 0.8561 (m-10) cc_final: 0.8321 (m-80) REVERT: K 31 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8181 (mp) REVERT: L 240 MET cc_start: 0.8343 (mmm) cc_final: 0.7976 (mmp) REVERT: L 269 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7319 (mm-30) REVERT: M 19 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7264 (mmm) REVERT: M 101 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8423 (pttm) REVERT: Q 3 LYS cc_start: 0.7377 (mtpt) cc_final: 0.6687 (mptm) REVERT: R 21 HIS cc_start: 0.7551 (t-170) cc_final: 0.7176 (t-90) REVERT: S 9 GLN cc_start: 0.6501 (mt0) cc_final: 0.6081 (tt0) REVERT: S 12 ASP cc_start: 0.7886 (t70) cc_final: 0.7590 (t70) REVERT: U 14 ARG cc_start: 0.6835 (ttt180) cc_final: 0.5762 (mtt180) REVERT: U 30 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7370 (ttm) REVERT: U 42 ASN cc_start: 0.8346 (t0) cc_final: 0.7713 (t0) REVERT: W 4 PHE cc_start: 0.7374 (m-80) cc_final: 0.6734 (m-80) REVERT: W 7 ILE cc_start: 0.8692 (tt) cc_final: 0.8174 (pt) REVERT: W 15 ARG cc_start: 0.5502 (ttm170) cc_final: 0.4252 (tmt-80) REVERT: W 33 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8288 (mp) REVERT: Z 15 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6657 (pm20) REVERT: Z 21 HIS cc_start: 0.7443 (t70) cc_final: 0.7119 (t70) REVERT: Z 25 MET cc_start: 0.6729 (ptt) cc_final: 0.6153 (ppp) REVERT: 4 30 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7595 (ttm) REVERT: 4 40 ASP cc_start: 0.7923 (m-30) cc_final: 0.7367 (t0) REVERT: 5 19 GLU cc_start: 0.6621 (tt0) cc_final: 0.6343 (mt-10) REVERT: 6 42 ASN cc_start: 0.6681 (t0) cc_final: 0.6428 (t0) REVERT: d 44 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8275 (mp) REVERT: e 3 LYS cc_start: 0.7634 (mttp) cc_final: 0.7050 (mppt) REVERT: e 12 ASP cc_start: 0.9002 (t70) cc_final: 0.8753 (t70) REVERT: g 18 GLN cc_start: 0.7521 (tt0) cc_final: 0.7279 (tp-100) REVERT: h 12 LEU cc_start: 0.1546 (OUTLIER) cc_final: 0.0846 (pp) REVERT: h 30 MET cc_start: 0.8515 (mmm) cc_final: 0.7904 (mpp) REVERT: h 34 TRP cc_start: 0.7651 (m100) cc_final: 0.7082 (t60) REVERT: h 53 TRP cc_start: 0.6469 (p90) cc_final: 0.6241 (p90) REVERT: i 29 VAL cc_start: 0.9089 (t) cc_final: 0.8740 (m) REVERT: i 40 ASP cc_start: 0.8167 (t70) cc_final: 0.7726 (t0) REVERT: l 8 SER cc_start: 0.8823 (p) cc_final: 0.8169 (t) REVERT: l 15 GLU cc_start: 0.8641 (pm20) cc_final: 0.7982 (mm-30) REVERT: m 44 MET cc_start: 0.8336 (mmm) cc_final: 0.7916 (mmm) REVERT: m 98 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8103 (mm-30) REVERT: m 136 MET cc_start: 0.7972 (mtm) cc_final: 0.7577 (ptp) REVERT: n 9 GLN cc_start: 0.7785 (mt0) cc_final: 0.7119 (mt0) REVERT: o 25 MET cc_start: 0.8519 (mmm) cc_final: 0.8251 (mmm) REVERT: p 17 PHE cc_start: 0.8554 (m-10) cc_final: 0.8319 (m-80) REVERT: p 31 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8172 (mp) REVERT: q 240 MET cc_start: 0.8336 (mmm) cc_final: 0.7960 (mmp) REVERT: q 269 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7324 (mm-30) REVERT: r 19 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7251 (mmm) REVERT: r 101 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8444 (pttm) REVERT: v 3 LYS cc_start: 0.7387 (mtpt) cc_final: 0.6699 (mptm) REVERT: w 21 HIS cc_start: 0.7546 (t-170) cc_final: 0.7170 (t-90) REVERT: x 9 GLN cc_start: 0.6507 (mt0) cc_final: 0.6082 (tt0) REVERT: x 12 ASP cc_start: 0.7896 (t70) cc_final: 0.7602 (t70) REVERT: z 14 ARG cc_start: 0.6831 (ttt180) cc_final: 0.5765 (mtt180) REVERT: z 30 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7381 (ttm) REVERT: z 42 ASN cc_start: 0.8336 (t0) cc_final: 0.7700 (t0) REVERT: AB 4 PHE cc_start: 0.7369 (m-80) cc_final: 0.6733 (m-80) REVERT: AB 7 ILE cc_start: 0.8692 (tt) cc_final: 0.8175 (pt) REVERT: AB 15 ARG cc_start: 0.5494 (ttm170) cc_final: 0.4249 (tmt-80) REVERT: AB 33 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8293 (mp) REVERT: AD 15 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6651 (pm20) REVERT: AD 21 HIS cc_start: 0.7445 (t70) cc_final: 0.7120 (t70) REVERT: AD 25 MET cc_start: 0.6735 (ptt) cc_final: 0.6159 (ppp) outliers start: 105 outliers final: 44 residues processed: 747 average time/residue: 0.3513 time to fit residues: 348.0010 Evaluate side-chains 708 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 646 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 44 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 128 SER Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain V residue 25 MET Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain 4 residue 30 MET Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain r residue 19 MET Chi-restraints excluded: chain r residue 29 ASN Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 128 SER Chi-restraints excluded: chain r residue 306 VAL Chi-restraints excluded: chain s residue 10 THR Chi-restraints excluded: chain t residue 2 SER Chi-restraints excluded: chain w residue 12 LEU Chi-restraints excluded: chain x residue 16 VAL Chi-restraints excluded: chain z residue 30 MET Chi-restraints excluded: chain AA residue 25 MET Chi-restraints excluded: chain AB residue 33 LEU Chi-restraints excluded: chain AB residue 36 LEU Chi-restraints excluded: chain AC residue 33 VAL Chi-restraints excluded: chain AD residue 15 GLU Chi-restraints excluded: chain AE residue 16 VAL Chi-restraints excluded: chain AE residue 45 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 184 optimal weight: 40.0000 chunk 52 optimal weight: 7.9990 chunk 419 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 433 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 225 optimal weight: 30.0000 chunk 421 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 21 HIS F 20 GLN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN M 29 ASN M 45 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 ASN 5 21 HIS k 20 GLN ** k 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 10 GLN r 29 ASN r 45 ASN ** r 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN ** w 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.151159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113957 restraints weight = 67022.316| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.75 r_work: 0.3314 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 48262 Z= 0.257 Angle : 0.878 13.767 66150 Z= 0.353 Chirality : 0.043 0.225 6344 Planarity : 0.004 0.044 8082 Dihedral : 18.906 179.937 9216 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.12 % Allowed : 20.62 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.12), residues: 4466 helix: 1.59 (0.09), residues: 3058 sheet: -0.67 (0.65), residues: 60 loop : -0.47 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 6 53 TYR 0.017 0.002 TYR M 303 PHE 0.036 0.002 PHE 6 25 TRP 0.031 0.002 TRP L 272 HIS 0.009 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00628 (48240) covalent geometry : angle 0.87824 (66150) hydrogen bonds : bond 0.05198 ( 2580) hydrogen bonds : angle 4.02398 ( 7434) Misc. bond : bond 0.00230 ( 22) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 694 time to evaluate : 0.905 Fit side-chains REVERT: 1 30 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7352 (ttm) REVERT: 2 19 GLU cc_start: 0.6598 (tt0) cc_final: 0.6346 (mt-10) REVERT: 3 42 ASN cc_start: 0.6424 (t0) cc_final: 0.6198 (t0) REVERT: 8 44 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8069 (mp) REVERT: 9 3 LYS cc_start: 0.7397 (mttp) cc_final: 0.6942 (mtmm) REVERT: 9 12 ASP cc_start: 0.9049 (t70) cc_final: 0.8768 (t70) REVERT: B 18 GLN cc_start: 0.7445 (tt0) cc_final: 0.7057 (tp-100) REVERT: C 30 MET cc_start: 0.8486 (mmm) cc_final: 0.7906 (mpp) REVERT: C 34 TRP cc_start: 0.7700 (m100) cc_final: 0.7076 (t60) REVERT: C 53 TRP cc_start: 0.6291 (p90) cc_final: 0.6001 (p90) REVERT: D 29 VAL cc_start: 0.8816 (t) cc_final: 0.8432 (m) REVERT: D 40 ASP cc_start: 0.8224 (t70) cc_final: 0.7530 (t0) REVERT: G 8 SER cc_start: 0.8721 (p) cc_final: 0.7994 (t) REVERT: H 38 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: H 44 MET cc_start: 0.8197 (mmm) cc_final: 0.7697 (mmm) REVERT: H 98 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7964 (mm-30) REVERT: H 136 MET cc_start: 0.7847 (mtm) cc_final: 0.7002 (ptp) REVERT: I 9 GLN cc_start: 0.7769 (mt0) cc_final: 0.7113 (mt0) REVERT: J 25 MET cc_start: 0.8255 (mmm) cc_final: 0.7934 (mmm) REVERT: K 5 TYR cc_start: 0.7133 (p90) cc_final: 0.6909 (p90) REVERT: L 203 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7205 (tptt) REVERT: L 240 MET cc_start: 0.7943 (mmm) cc_final: 0.7542 (mmp) REVERT: L 269 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7080 (mm-30) REVERT: M 19 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7132 (mmm) REVERT: M 108 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7773 (mtt180) REVERT: Q 3 LYS cc_start: 0.7082 (mtpt) cc_final: 0.6544 (mptm) REVERT: S 9 GLN cc_start: 0.6469 (mt0) cc_final: 0.6009 (tt0) REVERT: S 12 ASP cc_start: 0.7965 (t70) cc_final: 0.7618 (t70) REVERT: U 14 ARG cc_start: 0.6767 (ttt180) cc_final: 0.5715 (mtt180) REVERT: U 30 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7105 (ttm) REVERT: U 42 ASN cc_start: 0.8227 (t0) cc_final: 0.7558 (t0) REVERT: V 44 ILE cc_start: 0.8162 (mp) cc_final: 0.7959 (pt) REVERT: W 4 PHE cc_start: 0.7137 (m-80) cc_final: 0.6904 (m-80) REVERT: W 8 TRP cc_start: 0.7405 (m100) cc_final: 0.6634 (m-90) REVERT: W 15 ARG cc_start: 0.5451 (ttm170) cc_final: 0.4246 (tmt-80) REVERT: Z 15 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6635 (pm20) REVERT: a 36 LEU cc_start: 0.7264 (tp) cc_final: 0.7053 (mt) REVERT: b 46 ARG cc_start: 0.7906 (ttt180) cc_final: 0.7697 (ttt180) REVERT: 4 30 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7379 (ttm) REVERT: 5 19 GLU cc_start: 0.6600 (tt0) cc_final: 0.6351 (mt-10) REVERT: 6 42 ASN cc_start: 0.6432 (t0) cc_final: 0.6206 (t0) REVERT: d 44 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8069 (mp) REVERT: e 3 LYS cc_start: 0.7397 (mttp) cc_final: 0.6942 (mtmm) REVERT: e 12 ASP cc_start: 0.9045 (t70) cc_final: 0.8763 (t70) REVERT: g 18 GLN cc_start: 0.7460 (tt0) cc_final: 0.7071 (tp-100) REVERT: h 30 MET cc_start: 0.8484 (mmm) cc_final: 0.7906 (mpp) REVERT: h 34 TRP cc_start: 0.7699 (m100) cc_final: 0.7075 (t60) REVERT: h 53 TRP cc_start: 0.6264 (p90) cc_final: 0.5975 (p90) REVERT: i 29 VAL cc_start: 0.8819 (t) cc_final: 0.8433 (m) REVERT: i 40 ASP cc_start: 0.8217 (t70) cc_final: 0.7501 (t0) REVERT: l 8 SER cc_start: 0.8715 (p) cc_final: 0.7996 (t) REVERT: m 38 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: m 44 MET cc_start: 0.8221 (mmm) cc_final: 0.7722 (mmm) REVERT: m 98 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7957 (mm-30) REVERT: m 136 MET cc_start: 0.7824 (mtm) cc_final: 0.6982 (ptp) REVERT: n 9 GLN cc_start: 0.7764 (mt0) cc_final: 0.7112 (mt0) REVERT: o 25 MET cc_start: 0.8265 (mmm) cc_final: 0.7944 (mmm) REVERT: p 5 TYR cc_start: 0.7151 (p90) cc_final: 0.6927 (p90) REVERT: q 203 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7203 (tptt) REVERT: q 240 MET cc_start: 0.7956 (mmm) cc_final: 0.7551 (mmp) REVERT: q 269 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7070 (mm-30) REVERT: r 19 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7135 (mmm) REVERT: r 108 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7766 (mtt180) REVERT: v 3 LYS cc_start: 0.7076 (mtpt) cc_final: 0.6540 (mptm) REVERT: x 9 GLN cc_start: 0.6464 (mt0) cc_final: 0.6007 (tt0) REVERT: x 12 ASP cc_start: 0.7975 (t70) cc_final: 0.7628 (t70) REVERT: z 14 ARG cc_start: 0.6770 (ttt180) cc_final: 0.5714 (mtt180) REVERT: z 30 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7112 (ttm) REVERT: z 42 ASN cc_start: 0.8225 (t0) cc_final: 0.7554 (t0) REVERT: AA 44 ILE cc_start: 0.8169 (mp) cc_final: 0.7960 (pt) REVERT: AB 4 PHE cc_start: 0.7131 (m-80) cc_final: 0.6896 (m-80) REVERT: AB 8 TRP cc_start: 0.7397 (m100) cc_final: 0.6636 (m-90) REVERT: AB 15 ARG cc_start: 0.5454 (ttm170) cc_final: 0.4249 (tmt-80) REVERT: AB 33 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8240 (mp) REVERT: AD 15 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6635 (pm20) REVERT: AE 36 LEU cc_start: 0.7276 (tp) cc_final: 0.7064 (mt) REVERT: AF 46 ARG cc_start: 0.7933 (ttt180) cc_final: 0.7717 (ttt180) outliers start: 121 outliers final: 54 residues processed: 767 average time/residue: 0.3431 time to fit residues: 354.0403 Evaluate side-chains 714 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 645 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 44 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 128 SER Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain V residue 25 MET Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain 4 residue 30 MET Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain m residue 38 GLU Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain o residue 20 LEU Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain r residue 19 MET Chi-restraints excluded: chain r residue 108 ARG Chi-restraints excluded: chain r residue 128 SER Chi-restraints excluded: chain r residue 181 THR Chi-restraints excluded: chain r residue 306 VAL Chi-restraints excluded: chain s residue 10 THR Chi-restraints excluded: chain w residue 12 LEU Chi-restraints excluded: chain x residue 16 VAL Chi-restraints excluded: chain z residue 30 MET Chi-restraints excluded: chain AA residue 25 MET Chi-restraints excluded: chain AB residue 33 LEU Chi-restraints excluded: chain AB residue 36 LEU Chi-restraints excluded: chain AC residue 33 VAL Chi-restraints excluded: chain AD residue 15 GLU Chi-restraints excluded: chain AE residue 16 VAL Chi-restraints excluded: chain AE residue 45 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 245 optimal weight: 1.9990 chunk 324 optimal weight: 4.9990 chunk 425 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 218 optimal weight: 30.0000 chunk 75 optimal weight: 3.9990 chunk 415 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 337 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 377 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 21 HIS 7 20 GLN F 20 GLN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN M 29 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 32 HIS 5 21 HIS c 20 GLN k 20 GLN ** l 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 10 GLN r 29 ASN ** r 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN ** w 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 42 ASN ** AD 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 32 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120093 restraints weight = 66715.457| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.51 r_work: 0.3354 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 48262 Z= 0.167 Angle : 0.803 13.664 66150 Z= 0.322 Chirality : 0.040 0.225 6344 Planarity : 0.004 0.043 8082 Dihedral : 18.485 179.999 9216 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.76 % Allowed : 21.37 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.12), residues: 4466 helix: 1.78 (0.09), residues: 3048 sheet: -0.73 (0.66), residues: 60 loop : -0.43 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 6 53 TYR 0.018 0.001 TYR s 24 PHE 0.041 0.001 PHE 6 25 TRP 0.034 0.001 TRP 1 43 HIS 0.011 0.001 HIS N 21 Details of bonding type rmsd covalent geometry : bond 0.00399 (48240) covalent geometry : angle 0.80252 (66150) hydrogen bonds : bond 0.04802 ( 2580) hydrogen bonds : angle 3.90948 ( 7434) Misc. bond : bond 0.00148 ( 22) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 683 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 25 MET cc_start: 0.8727 (mmm) cc_final: 0.8486 (mmp) REVERT: 1 30 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7446 (ttm) REVERT: 2 19 GLU cc_start: 0.6609 (tt0) cc_final: 0.6322 (mt-10) REVERT: 3 42 ASN cc_start: 0.6777 (t0) cc_final: 0.6525 (t0) REVERT: 8 44 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8197 (mp) REVERT: 9 3 LYS cc_start: 0.7662 (mttp) cc_final: 0.7043 (mppt) REVERT: 9 12 ASP cc_start: 0.9027 (t70) cc_final: 0.8798 (t70) REVERT: A 1 MET cc_start: 0.8097 (ttm) cc_final: 0.7876 (ttp) REVERT: A 34 ILE cc_start: 0.9009 (mt) cc_final: 0.8764 (mm) REVERT: B 18 GLN cc_start: 0.7746 (tt0) cc_final: 0.7355 (tp-100) REVERT: C 30 MET cc_start: 0.8497 (mmm) cc_final: 0.7713 (mmp) REVERT: C 34 TRP cc_start: 0.7688 (m100) cc_final: 0.7096 (t60) REVERT: C 53 TRP cc_start: 0.6572 (p90) cc_final: 0.6314 (p90) REVERT: D 29 VAL cc_start: 0.9085 (t) cc_final: 0.8719 (m) REVERT: D 40 ASP cc_start: 0.8180 (t70) cc_final: 0.7858 (t0) REVERT: G 8 SER cc_start: 0.8832 (p) cc_final: 0.8184 (t) REVERT: H 38 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: H 44 MET cc_start: 0.8363 (mmm) cc_final: 0.7995 (mmm) REVERT: H 98 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8201 (mm-30) REVERT: H 136 MET cc_start: 0.7958 (mtm) cc_final: 0.7354 (ptp) REVERT: J 25 MET cc_start: 0.8506 (mmm) cc_final: 0.8170 (mmm) REVERT: K 5 TYR cc_start: 0.7159 (p90) cc_final: 0.6938 (p90) REVERT: L 269 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7333 (mm-30) REVERT: M 19 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7188 (mmm) REVERT: M 101 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8417 (pttm) REVERT: M 108 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7972 (mtt180) REVERT: P 18 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7292 (tp40) REVERT: Q 3 LYS cc_start: 0.7129 (mtpt) cc_final: 0.6625 (mptm) REVERT: S 9 GLN cc_start: 0.6518 (mt0) cc_final: 0.5964 (tt0) REVERT: S 12 ASP cc_start: 0.8055 (t70) cc_final: 0.7740 (t70) REVERT: U 14 ARG cc_start: 0.6872 (ttt180) cc_final: 0.5806 (mtt180) REVERT: U 30 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7283 (ttm) REVERT: U 42 ASN cc_start: 0.8330 (t0) cc_final: 0.7703 (t0) REVERT: W 4 PHE cc_start: 0.7437 (m-80) cc_final: 0.5747 (m-80) REVERT: W 7 ILE cc_start: 0.8716 (tt) cc_final: 0.7619 (pt) REVERT: W 15 ARG cc_start: 0.5435 (ttm170) cc_final: 0.4155 (tmt-80) REVERT: Z 15 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6701 (pm20) REVERT: Z 25 MET cc_start: 0.6734 (ptt) cc_final: 0.6486 (ppp) REVERT: Y 25 MET cc_start: 0.8743 (mmm) cc_final: 0.8501 (mmp) REVERT: 4 30 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7464 (ttm) REVERT: 5 19 GLU cc_start: 0.6607 (tt0) cc_final: 0.6316 (mt-10) REVERT: 6 42 ASN cc_start: 0.6777 (t0) cc_final: 0.6524 (t0) REVERT: d 44 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8185 (mp) REVERT: e 3 LYS cc_start: 0.7685 (mttp) cc_final: 0.7064 (mppt) REVERT: e 12 ASP cc_start: 0.9021 (t70) cc_final: 0.8791 (t70) REVERT: f 1 MET cc_start: 0.8082 (ttm) cc_final: 0.7864 (ttp) REVERT: f 34 ILE cc_start: 0.9007 (mt) cc_final: 0.8767 (mm) REVERT: g 18 GLN cc_start: 0.7754 (tt0) cc_final: 0.7363 (tp-100) REVERT: h 30 MET cc_start: 0.8497 (mmm) cc_final: 0.7713 (mmp) REVERT: h 34 TRP cc_start: 0.7684 (m100) cc_final: 0.7099 (t60) REVERT: h 53 TRP cc_start: 0.6569 (p90) cc_final: 0.6312 (p90) REVERT: i 29 VAL cc_start: 0.9083 (t) cc_final: 0.8715 (m) REVERT: i 40 ASP cc_start: 0.8185 (t70) cc_final: 0.7860 (t0) REVERT: l 8 SER cc_start: 0.8821 (p) cc_final: 0.8169 (t) REVERT: m 38 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: m 44 MET cc_start: 0.8385 (mmm) cc_final: 0.8022 (mmm) REVERT: m 98 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8180 (mm-30) REVERT: m 136 MET cc_start: 0.7950 (mtm) cc_final: 0.7360 (ptp) REVERT: o 25 MET cc_start: 0.8513 (mmm) cc_final: 0.8174 (mmm) REVERT: p 5 TYR cc_start: 0.7160 (p90) cc_final: 0.6936 (p90) REVERT: q 269 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7369 (mm-30) REVERT: r 19 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7184 (mmm) REVERT: r 101 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8421 (pttm) REVERT: r 108 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7964 (mtt180) REVERT: u 18 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7297 (tp40) REVERT: v 3 LYS cc_start: 0.7125 (mtpt) cc_final: 0.6618 (mptm) REVERT: x 9 GLN cc_start: 0.6519 (mt0) cc_final: 0.5967 (tt0) REVERT: x 12 ASP cc_start: 0.8062 (t70) cc_final: 0.7748 (t70) REVERT: z 14 ARG cc_start: 0.6871 (ttt180) cc_final: 0.5807 (mtt180) REVERT: z 30 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7304 (ttm) REVERT: z 42 ASN cc_start: 0.8346 (t0) cc_final: 0.7719 (t0) REVERT: AB 4 PHE cc_start: 0.7422 (m-80) cc_final: 0.5725 (m-80) REVERT: AB 7 ILE cc_start: 0.8713 (tt) cc_final: 0.7614 (pt) REVERT: AB 15 ARG cc_start: 0.5446 (ttm170) cc_final: 0.4156 (tmt-80) REVERT: AD 15 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6706 (pm20) REVERT: AD 25 MET cc_start: 0.6732 (ptt) cc_final: 0.6485 (ppp) outliers start: 107 outliers final: 49 residues processed: 741 average time/residue: 0.3376 time to fit residues: 333.5805 Evaluate side-chains 704 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 639 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 44 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 128 SER Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain 4 residue 30 MET Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain m residue 38 GLU Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain o residue 20 LEU Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain r residue 19 MET Chi-restraints excluded: chain r residue 29 ASN Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 108 ARG Chi-restraints excluded: chain r residue 128 SER Chi-restraints excluded: chain r residue 181 THR Chi-restraints excluded: chain r residue 306 VAL Chi-restraints excluded: chain s residue 10 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain w residue 12 LEU Chi-restraints excluded: chain x residue 16 VAL Chi-restraints excluded: chain z residue 30 MET Chi-restraints excluded: chain AB residue 33 LEU Chi-restraints excluded: chain AB residue 36 LEU Chi-restraints excluded: chain AC residue 33 VAL Chi-restraints excluded: chain AD residue 15 GLU Chi-restraints excluded: chain AE residue 45 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 217 optimal weight: 5.9990 chunk 329 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 269 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 270 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 21 HIS A 42 ASN F 20 GLN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN M 10 GLN M 29 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 21 HIS f 42 ASN i 9 GLN k 20 GLN ** l 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 9 GLN r 10 GLN r 29 ASN ** r 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN ** w 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 32 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.156620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120095 restraints weight = 66607.951| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.80 r_work: 0.3385 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 48262 Z= 0.133 Angle : 0.764 13.438 66150 Z= 0.310 Chirality : 0.040 0.301 6344 Planarity : 0.003 0.042 8082 Dihedral : 17.996 179.956 9214 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.11 % Allowed : 21.93 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.12), residues: 4466 helix: 1.87 (0.09), residues: 3052 sheet: -0.58 (0.67), residues: 60 loop : -0.34 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 53 TYR 0.015 0.001 TYR r 303 PHE 0.042 0.001 PHE 6 25 TRP 0.056 0.001 TRP W 8 HIS 0.013 0.001 HIS N 21 Details of bonding type rmsd covalent geometry : bond 0.00312 (48240) covalent geometry : angle 0.76393 (66150) hydrogen bonds : bond 0.04535 ( 2580) hydrogen bonds : angle 3.86131 ( 7434) Misc. bond : bond 0.00102 ( 22) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 689 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 30 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7273 (ttt) REVERT: 2 19 GLU cc_start: 0.6546 (tt0) cc_final: 0.6263 (mt-10) REVERT: 8 40 ILE cc_start: 0.8926 (mt) cc_final: 0.8698 (mm) REVERT: 8 44 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8186 (mp) REVERT: 9 3 LYS cc_start: 0.7352 (mttp) cc_final: 0.6773 (mppt) REVERT: 9 12 ASP cc_start: 0.8957 (t70) cc_final: 0.8623 (t70) REVERT: A 34 ILE cc_start: 0.8770 (mt) cc_final: 0.8483 (mm) REVERT: B 18 GLN cc_start: 0.7295 (tt0) cc_final: 0.6998 (tp-100) REVERT: C 30 MET cc_start: 0.8399 (mmm) cc_final: 0.7846 (mmm) REVERT: C 34 TRP cc_start: 0.7678 (m100) cc_final: 0.7079 (t60) REVERT: C 53 TRP cc_start: 0.6378 (p90) cc_final: 0.6031 (p90) REVERT: D 29 VAL cc_start: 0.8828 (t) cc_final: 0.8431 (m) REVERT: D 40 ASP cc_start: 0.8146 (t70) cc_final: 0.7798 (t0) REVERT: G 8 SER cc_start: 0.8750 (p) cc_final: 0.8012 (t) REVERT: G 25 MET cc_start: 0.8581 (mmt) cc_final: 0.8270 (mmm) REVERT: H 98 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8134 (mm-30) REVERT: H 136 MET cc_start: 0.7609 (mtm) cc_final: 0.7140 (ptp) REVERT: I 41 TYR cc_start: 0.9179 (m-80) cc_final: 0.8934 (m-80) REVERT: J 25 MET cc_start: 0.8179 (mmm) cc_final: 0.7789 (mmm) REVERT: L 240 MET cc_start: 0.8038 (mmm) cc_final: 0.7638 (mmp) REVERT: L 255 ILE cc_start: 0.8664 (mt) cc_final: 0.8344 (mm) REVERT: L 269 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7187 (mm-30) REVERT: M 19 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7053 (mmm) REVERT: M 65 VAL cc_start: 0.8160 (t) cc_final: 0.7791 (p) REVERT: M 101 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8199 (pttm) REVERT: M 108 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7901 (mtt180) REVERT: N 12 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5765 (tp) REVERT: P 19 GLU cc_start: 0.7369 (pt0) cc_final: 0.6790 (tm-30) REVERT: P 25 MET cc_start: 0.5640 (tpp) cc_final: 0.5428 (tpp) REVERT: Q 3 LYS cc_start: 0.7010 (mtpt) cc_final: 0.6509 (mptm) REVERT: R 21 HIS cc_start: 0.7744 (t-170) cc_final: 0.7421 (t-90) REVERT: S 9 GLN cc_start: 0.6408 (mt0) cc_final: 0.5804 (tt0) REVERT: S 12 ASP cc_start: 0.7694 (t70) cc_final: 0.7436 (t70) REVERT: U 14 ARG cc_start: 0.6710 (ttt180) cc_final: 0.5569 (mtm110) REVERT: U 30 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6993 (ttm) REVERT: U 42 ASN cc_start: 0.8126 (t0) cc_final: 0.7459 (t0) REVERT: W 4 PHE cc_start: 0.7311 (m-80) cc_final: 0.6928 (m-80) REVERT: W 15 ARG cc_start: 0.5424 (ttm170) cc_final: 0.4212 (tmt-80) REVERT: W 33 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8223 (mp) REVERT: Z 15 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: Z 25 MET cc_start: 0.6910 (ptt) cc_final: 0.6542 (ppp) REVERT: a 36 LEU cc_start: 0.7709 (tp) cc_final: 0.7369 (mt) REVERT: 4 30 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7273 (ttt) REVERT: 5 19 GLU cc_start: 0.6541 (tt0) cc_final: 0.6253 (mt-10) REVERT: d 40 ILE cc_start: 0.8921 (mt) cc_final: 0.8692 (mm) REVERT: d 44 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8175 (mp) REVERT: e 3 LYS cc_start: 0.7351 (mttp) cc_final: 0.6779 (mppt) REVERT: e 12 ASP cc_start: 0.8963 (t70) cc_final: 0.8626 (t70) REVERT: f 34 ILE cc_start: 0.8760 (mt) cc_final: 0.8475 (mm) REVERT: g 18 GLN cc_start: 0.7296 (tt0) cc_final: 0.6997 (tp-100) REVERT: h 30 MET cc_start: 0.8405 (mmm) cc_final: 0.7846 (mmm) REVERT: h 34 TRP cc_start: 0.7677 (m100) cc_final: 0.7081 (t60) REVERT: h 53 TRP cc_start: 0.6383 (p90) cc_final: 0.6038 (p90) REVERT: i 29 VAL cc_start: 0.8814 (t) cc_final: 0.8417 (m) REVERT: i 40 ASP cc_start: 0.8145 (t70) cc_final: 0.7795 (t0) REVERT: l 8 SER cc_start: 0.8746 (p) cc_final: 0.8016 (t) REVERT: l 25 MET cc_start: 0.8589 (mmt) cc_final: 0.8275 (mmm) REVERT: m 98 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8147 (mm-30) REVERT: m 136 MET cc_start: 0.7602 (mtm) cc_final: 0.7133 (ptp) REVERT: n 41 TYR cc_start: 0.9179 (m-80) cc_final: 0.8925 (m-80) REVERT: o 25 MET cc_start: 0.8224 (mmm) cc_final: 0.7824 (mmm) REVERT: q 240 MET cc_start: 0.8022 (mmm) cc_final: 0.7630 (mmp) REVERT: q 255 ILE cc_start: 0.8675 (mt) cc_final: 0.8349 (mm) REVERT: q 269 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7201 (mm-30) REVERT: r 19 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7058 (mmm) REVERT: r 65 VAL cc_start: 0.8180 (t) cc_final: 0.7798 (p) REVERT: r 101 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8194 (pttm) REVERT: r 108 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7891 (mtt180) REVERT: s 12 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5755 (tp) REVERT: u 19 GLU cc_start: 0.7372 (pt0) cc_final: 0.6791 (tm-30) REVERT: u 25 MET cc_start: 0.5636 (tpp) cc_final: 0.5420 (tpp) REVERT: v 3 LYS cc_start: 0.7012 (mtpt) cc_final: 0.6509 (mptm) REVERT: w 21 HIS cc_start: 0.7742 (t-170) cc_final: 0.7423 (t-90) REVERT: x 9 GLN cc_start: 0.6412 (mt0) cc_final: 0.5805 (tt0) REVERT: x 12 ASP cc_start: 0.7692 (t70) cc_final: 0.7432 (t70) REVERT: z 14 ARG cc_start: 0.6706 (ttt180) cc_final: 0.5567 (mtm110) REVERT: z 30 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7008 (ttm) REVERT: z 42 ASN cc_start: 0.8118 (t0) cc_final: 0.7455 (t0) REVERT: AB 4 PHE cc_start: 0.7292 (m-80) cc_final: 0.6910 (m-80) REVERT: AB 15 ARG cc_start: 0.5426 (ttm170) cc_final: 0.4208 (tmt-80) REVERT: AD 15 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6670 (pm20) REVERT: AD 25 MET cc_start: 0.6904 (ptt) cc_final: 0.6538 (ppp) REVERT: AE 36 LEU cc_start: 0.7705 (tp) cc_final: 0.7369 (mt) outliers start: 82 outliers final: 39 residues processed: 738 average time/residue: 0.3283 time to fit residues: 323.9430 Evaluate side-chains 688 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 632 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 44 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 40 ILE Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain 4 residue 30 MET Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain o residue 20 LEU Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain r residue 19 MET Chi-restraints excluded: chain r residue 29 ASN Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 108 ARG Chi-restraints excluded: chain r residue 181 THR Chi-restraints excluded: chain r residue 306 VAL Chi-restraints excluded: chain s residue 10 THR Chi-restraints excluded: chain s residue 12 LEU Chi-restraints excluded: chain w residue 12 LEU Chi-restraints excluded: chain x residue 16 VAL Chi-restraints excluded: chain z residue 30 MET Chi-restraints excluded: chain AB residue 33 LEU Chi-restraints excluded: chain AD residue 15 GLU Chi-restraints excluded: chain AD residue 40 ILE Chi-restraints excluded: chain AE residue 45 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 147 optimal weight: 2.9990 chunk 403 optimal weight: 40.0000 chunk 149 optimal weight: 0.9990 chunk 335 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 349 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 331 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 21 HIS A 42 ASN D 9 GLN F 20 GLN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN M 29 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 GLN ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 21 HIS f 42 ASN k 20 GLN ** l 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 10 GLN r 29 ASN ** r 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN ** w 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 23 GLN ** AD 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 32 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.156946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120271 restraints weight = 66871.353| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.61 r_work: 0.3384 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 48262 Z= 0.120 Angle : 0.744 13.281 66150 Z= 0.304 Chirality : 0.039 0.271 6344 Planarity : 0.003 0.041 8082 Dihedral : 17.651 179.907 9214 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.88 % Allowed : 22.58 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.12), residues: 4466 helix: 1.95 (0.09), residues: 3062 sheet: 0.61 (1.30), residues: 20 loop : -0.32 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 3 53 TYR 0.014 0.001 TYR M 303 PHE 0.043 0.001 PHE 3 25 TRP 0.057 0.001 TRP W 8 HIS 0.009 0.001 HIS N 21 Details of bonding type rmsd covalent geometry : bond 0.00274 (48240) covalent geometry : angle 0.74397 (66150) hydrogen bonds : bond 0.04374 ( 2580) hydrogen bonds : angle 3.83117 ( 7434) Misc. bond : bond 0.00074 ( 22) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8932 Ramachandran restraints generated. 4466 Oldfield, 0 Emsley, 4466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 671 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 19 GLU cc_start: 0.6465 (tt0) cc_final: 0.6258 (mt-10) REVERT: 8 25 MET cc_start: 0.8227 (mmt) cc_final: 0.7974 (mmp) REVERT: 8 40 ILE cc_start: 0.9055 (mt) cc_final: 0.8855 (mm) REVERT: 9 3 LYS cc_start: 0.7481 (mttp) cc_final: 0.6904 (mppt) REVERT: 9 12 ASP cc_start: 0.8851 (t70) cc_final: 0.8549 (t70) REVERT: A 3 LYS cc_start: 0.8725 (mttm) cc_final: 0.8237 (mtpp) REVERT: A 34 ILE cc_start: 0.8911 (mt) cc_final: 0.8635 (mm) REVERT: B 18 GLN cc_start: 0.7459 (tt0) cc_final: 0.7151 (tp-100) REVERT: C 12 LEU cc_start: 0.1116 (OUTLIER) cc_final: 0.0417 (pp) REVERT: C 30 MET cc_start: 0.8292 (mmm) cc_final: 0.7790 (mmm) REVERT: C 34 TRP cc_start: 0.7643 (m100) cc_final: 0.7049 (t60) REVERT: C 53 TRP cc_start: 0.6500 (p90) cc_final: 0.6095 (p90) REVERT: D 29 VAL cc_start: 0.8987 (t) cc_final: 0.8620 (m) REVERT: G 8 SER cc_start: 0.8806 (p) cc_final: 0.8134 (t) REVERT: H 98 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8244 (mm-30) REVERT: H 136 MET cc_start: 0.7689 (mtm) cc_final: 0.7392 (ptp) REVERT: J 25 MET cc_start: 0.8249 (mmm) cc_final: 0.7888 (mmm) REVERT: L 240 MET cc_start: 0.8225 (mmm) cc_final: 0.7843 (mmp) REVERT: L 255 ILE cc_start: 0.8788 (mt) cc_final: 0.8529 (mm) REVERT: L 269 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7329 (mm-30) REVERT: M 19 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7037 (mmm) REVERT: M 65 VAL cc_start: 0.8340 (t) cc_final: 0.7965 (p) REVERT: M 101 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8392 (pttm) REVERT: M 108 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7921 (mtt180) REVERT: N 12 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.5962 (tp) REVERT: Q 3 LYS cc_start: 0.7038 (mtpt) cc_final: 0.6421 (mptm) REVERT: R 21 HIS cc_start: 0.7754 (t-170) cc_final: 0.7443 (t-90) REVERT: S 12 ASP cc_start: 0.7625 (t70) cc_final: 0.7388 (t70) REVERT: U 14 ARG cc_start: 0.6800 (ttt180) cc_final: 0.5599 (mtm110) REVERT: U 30 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6959 (ttm) REVERT: U 34 ILE cc_start: 0.8303 (mt) cc_final: 0.8037 (mp) REVERT: U 42 ASN cc_start: 0.8108 (t0) cc_final: 0.7474 (t0) REVERT: V 29 TRP cc_start: 0.7631 (m100) cc_final: 0.6432 (m-10) REVERT: W 4 PHE cc_start: 0.7199 (m-80) cc_final: 0.6984 (m-80) REVERT: W 15 ARG cc_start: 0.5259 (ttm170) cc_final: 0.4076 (tmt-80) REVERT: W 33 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8158 (mp) REVERT: Z 15 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6649 (pm20) REVERT: Z 25 MET cc_start: 0.6883 (ptt) cc_final: 0.6588 (ppp) REVERT: 5 19 GLU cc_start: 0.6463 (tt0) cc_final: 0.6257 (mt-10) REVERT: d 25 MET cc_start: 0.8256 (mmt) cc_final: 0.7999 (mmp) REVERT: d 40 ILE cc_start: 0.9041 (mt) cc_final: 0.8836 (mm) REVERT: e 3 LYS cc_start: 0.7496 (mttp) cc_final: 0.6923 (mppt) REVERT: e 12 ASP cc_start: 0.8859 (t70) cc_final: 0.8553 (t70) REVERT: f 3 LYS cc_start: 0.8736 (mttm) cc_final: 0.8247 (mtpp) REVERT: f 34 ILE cc_start: 0.8905 (mt) cc_final: 0.8636 (mm) REVERT: g 18 GLN cc_start: 0.7469 (tt0) cc_final: 0.7159 (tp-100) REVERT: h 12 LEU cc_start: 0.1095 (OUTLIER) cc_final: 0.0406 (pp) REVERT: h 30 MET cc_start: 0.8294 (mmm) cc_final: 0.7790 (mmm) REVERT: h 34 TRP cc_start: 0.7638 (m100) cc_final: 0.7048 (t60) REVERT: h 53 TRP cc_start: 0.6510 (p90) cc_final: 0.6090 (p90) REVERT: i 29 VAL cc_start: 0.8990 (t) cc_final: 0.8625 (m) REVERT: l 8 SER cc_start: 0.8800 (p) cc_final: 0.8122 (t) REVERT: m 98 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8252 (mm-30) REVERT: m 136 MET cc_start: 0.7693 (mtm) cc_final: 0.7388 (ptp) REVERT: o 25 MET cc_start: 0.8249 (mmm) cc_final: 0.7884 (mmm) REVERT: q 240 MET cc_start: 0.8216 (mmm) cc_final: 0.7836 (mmp) REVERT: q 255 ILE cc_start: 0.8783 (mt) cc_final: 0.8523 (mm) REVERT: q 269 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7342 (mm-30) REVERT: r 19 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7032 (mmm) REVERT: r 65 VAL cc_start: 0.8346 (t) cc_final: 0.7961 (p) REVERT: r 101 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8387 (pttm) REVERT: r 108 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7924 (mtt180) REVERT: s 12 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5962 (tp) REVERT: v 3 LYS cc_start: 0.7037 (mtpt) cc_final: 0.6420 (mptm) REVERT: w 21 HIS cc_start: 0.7750 (t-170) cc_final: 0.7438 (t-90) REVERT: x 12 ASP cc_start: 0.7631 (t70) cc_final: 0.7394 (t70) REVERT: z 14 ARG cc_start: 0.6791 (ttt180) cc_final: 0.5590 (mtm110) REVERT: z 30 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7038 (ttm) REVERT: z 42 ASN cc_start: 0.8107 (t0) cc_final: 0.7473 (t0) REVERT: AA 29 TRP cc_start: 0.7624 (m100) cc_final: 0.6439 (m-10) REVERT: AB 4 PHE cc_start: 0.7183 (m-80) cc_final: 0.6967 (m-80) REVERT: AB 15 ARG cc_start: 0.5305 (ttm170) cc_final: 0.4098 (tmt-80) REVERT: AD 15 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6645 (pm20) REVERT: AD 25 MET cc_start: 0.6880 (ptt) cc_final: 0.6589 (ppp) outliers start: 73 outliers final: 33 residues processed: 712 average time/residue: 0.3196 time to fit residues: 307.1324 Evaluate side-chains 682 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 634 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain o residue 20 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 217 PHE Chi-restraints excluded: chain r residue 19 MET Chi-restraints excluded: chain r residue 29 ASN Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 108 ARG Chi-restraints excluded: chain r residue 181 THR Chi-restraints excluded: chain r residue 306 VAL Chi-restraints excluded: chain s residue 10 THR Chi-restraints excluded: chain s residue 12 LEU Chi-restraints excluded: chain w residue 12 LEU Chi-restraints excluded: chain x residue 16 VAL Chi-restraints excluded: chain z residue 30 MET Chi-restraints excluded: chain AB residue 33 LEU Chi-restraints excluded: chain AD residue 15 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 109 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 419 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 chunk 363 optimal weight: 0.5980 chunk 337 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 21 HIS F 20 GLN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN M 10 GLN M 29 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 32 HIS 5 21 HIS k 20 GLN ** l 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 9 GLN r 10 GLN r 29 ASN ** r 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN ** w 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 32 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.156575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123624 restraints weight = 66950.473| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.46 r_work: 0.3347 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 48262 Z= 0.149 Angle : 0.770 12.959 66150 Z= 0.319 Chirality : 0.040 0.285 6344 Planarity : 0.003 0.040 8082 Dihedral : 17.678 179.932 9214 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.68 % Allowed : 22.89 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.12), residues: 4466 helix: 1.88 (0.09), residues: 3064 sheet: -1.56 (0.80), residues: 40 loop : -0.33 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 53 TYR 0.022 0.001 TYR Y 24 PHE 0.043 0.001 PHE 6 25 TRP 0.049 0.001 TRP W 8 HIS 0.009 0.001 HIS N 21 Details of bonding type rmsd covalent geometry : bond 0.00355 (48240) covalent geometry : angle 0.77046 (66150) hydrogen bonds : bond 0.04548 ( 2580) hydrogen bonds : angle 3.85963 ( 7434) Misc. bond : bond 0.00119 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13614.15 seconds wall clock time: 232 minutes 20.82 seconds (13940.82 seconds total)