Starting phenix.real_space_refine on Mon Sep 14 18:28:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6osy_20189/09_2026/6osy_20189.cif Found real_map, /net/cci-nas-00/data/ceres_data/6osy_20189/09_2026/6osy_20189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6osy_20189/09_2026/6osy_20189.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6osy_20189/09_2026/6osy_20189.cif" model { file = "/net/cci-nas-00/data/ceres_data/6osy_20189/09_2026/6osy_20189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6osy_20189/09_2026/6osy_20189.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6osy_20189/09_2026/6osy_20189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6osy_20189/09_2026/6osy_20189.map" } resolution = 4.3 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= 0.006 sd= 0.138 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: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 20328 2.51 5 N 5316 2.21 5 O 6645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32463 Number of models: 1 Model: "" Number of chains: 78 Chain: "2" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "5" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "7" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "8" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "B" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "C" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "I" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "J" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 98} Chain: "K" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 98} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "O" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "P" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "Q" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "S" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 98} Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "m" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "CA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "DA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "EA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "FA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "GA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "HA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "IA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "JA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "2" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.29, per 1000 atoms: 0.22 Number of scatterers: 32463 At special positions: 0 Unit cell: (157.768, 157.768, 154.548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 6645 8.00 N 5316 7.00 C 20328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS 2 54 " - pdb=" SG CYS 2 74 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.01 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.05 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 22 " - pdb=" SG CYS 8 92 " distance=2.02 Simple disulfide: pdb=" SG CYS 8 98 " - pdb=" SG CYS 8 100A" distance=2.02 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.01 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.04 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.02 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.01 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.05 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 100A" distance=2.02 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.02 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.01 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.05 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 98 " - pdb=" SG CYS P 100A" distance=2.02 Simple disulfide: pdb=" SG CYS Q 598 " - pdb=" SG CYS Q 604 " distance=2.01 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.04 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.04 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=0, symmetry=0 Links applied ALPHA1-2 " MAN a 4 " - " MAN a 5 " " MAN g 4 " - " MAN g 5 " " MAN g 5 " - " MAN g 6 " " MAN q 4 " - " MAN q 5 " " MAN w 4 " - " MAN w 5 " " MAN w 5 " - " MAN w 6 " " MANBA 4 " - " MANBA 5 " " MANHA 4 " - " MANHA 5 " " MANHA 5 " - " MANHA 6 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 3 3 " - " MAN 3 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " " BMA e 3 " - " MAN e 4 " " BMA g 3 " - " MAN g 4 " " MAN g 7 " - " MAN g 8 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 4 " " BMA q 3 " - " MAN q 4 " " BMA u 3 " - " MAN u 4 " " BMA w 3 " - " MAN w 4 " " MAN w 7 " - " MAN w 8 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " " BMABA 3 " - " MANBA 4 " " BMAFA 3 " - " MANFA 4 " " BMAHA 3 " - " MANHA 4 " " MANHA 7 " - " MANHA 8 " " BMAJA 3 " - " MANJA 4 " ALPHA1-6 " BMA 3 3 " - " MAN 3 5 " " BMA 9 3 " - " MAN 9 4 " " BMA W 3 " - " MAN W 5 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 6 " " BMA e 3 " - " MAN e 5 " " BMA g 3 " - " MAN g 7 " " MAN g 7 " - " MAN g 9 " " BMA m 3 " - " MAN m 5 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 6 " " BMA u 3 " - " MAN u 5 " " BMA w 3 " - " MAN w 7 " " MAN w 7 " - " MAN w 9 " " BMABA 3 " - " MANBA 6 " " BMAFA 3 " - " MANFA 5 " " BMAHA 3 " - " MANHA 7 " " MANHA 7 " - " MANHA 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " NAG-ASN " NAG 0 1 " - " ASN K 133 " " NAG 1 1 " - " ASN K 137 " " NAG 2 635 " - " ASN 2 355 " " NAG 3 1 " - " ASN K 156 " " NAG 4 1 " - " ASN K 160 " " NAG 9 1 " - " ASN K 197 " " NAG A 701 " - " ASN A 637 " " NAG A 702 " - " ASN A 611 " " NAG B 635 " - " ASN B 355 " " NAG G 701 " - " ASN G 637 " " NAG G 702 " - " ASN G 611 " " NAG K 635 " - " ASN K 355 " " NAG Q 701 " - " ASN Q 637 " " NAG Q 702 " - " ASN Q 611 " " NAG T 1 " - " ASN 2 88 " " NAG U 1 " - " ASN 2 133 " " NAG V 1 " - " ASN 2 137 " " NAG W 1 " - " ASN 2 156 " " NAG X 1 " - " ASN 2 160 " " NAG Y 1 " - " ASN 2 197 " " NAG Z 1 " - " ASN 2 234 " " NAG a 1 " - " ASN 2 262 " " NAG b 1 " - " ASN 2 295 " " NAG c 1 " - " ASN 2 301 " " NAG d 1 " - " ASN 2 363 " " NAG e 1 " - " ASN 2 386 " " NAG f 1 " - " ASN 2 392 " " NAG g 1 " - " ASN 2 332 " " NAG h 1 " - " ASN 2 448 " " NAG i 1 " - " ASN 2 276 " " NAG j 1 " - " ASN B 88 " " NAG k 1 " - " ASN B 133 " " NAG l 1 " - " ASN B 137 " " NAG m 1 " - " ASN B 156 " " NAG n 1 " - " ASN B 160 " " NAG o 1 " - " ASN B 197 " " NAG p 1 " - " ASN B 234 " " NAG q 1 " - " ASN B 262 " " NAG r 1 " - " ASN B 295 " " NAG s 1 " - " ASN B 301 " " NAG t 1 " - " ASN B 363 " " NAG u 1 " - " ASN B 386 " " NAG v 1 " - " ASN B 392 " " NAG w 1 " - " ASN B 332 " " NAG x 1 " - " ASN B 448 " " NAG y 1 " - " ASN B 276 " " NAG z 1 " - " ASN K 88 " " NAGAA 1 " - " ASN K 234 " " NAGBA 1 " - " ASN K 262 " " NAGCA 1 " - " ASN K 295 " " NAGDA 1 " - " ASN K 301 " " NAGEA 1 " - " ASN K 363 " " NAGFA 1 " - " ASN K 386 " " NAGGA 1 " - " ASN K 392 " " NAGHA 1 " - " ASN K 332 " " NAGIA 1 " - " ASN K 448 " " NAGJA 1 " - " ASN K 276 " Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 72 sheets defined 14.1% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain '2' and resid 58 through 62 removed outlier: 3.565A pdb=" N GLU 2 62 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 115 removed outlier: 3.505A pdb=" N MET 2 104 " --> pdb=" O MET 2 100 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 126 removed outlier: 4.012A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 351 through 353 No H-bonds generated for 'chain '2' and resid 351 through 353' Processing helix chain '2' and resid 368 through 373 removed outlier: 3.836A pdb=" N THR 2 372 " --> pdb=" O ASP 2 368 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR 2 373 " --> pdb=" O LEU 2 369 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 368 through 373' Processing helix chain '2' and resid 387 through 390 removed outlier: 3.795A pdb=" N LEU 2 390 " --> pdb=" O THR 2 387 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 387 through 390' Processing helix chain '2' and resid 474 through 479 removed outlier: 3.882A pdb=" N ASP 2 477 " --> pdb=" O ASP 2 474 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN 2 478 " --> pdb=" O MET 2 475 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 86 Processing helix chain '5' and resid 100D through 100H removed outlier: 3.921A pdb=" N PHE 5 100G" --> pdb=" O VAL 5 100D" (cutoff:3.500A) Processing helix chain '6' and resid 79 through 83 Processing helix chain '7' and resid 78 through 82 removed outlier: 3.762A pdb=" N ASP 7 81 " --> pdb=" O ASP 7 78 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE 7 82 " --> pdb=" O ARG 7 79 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 78 through 82' Processing helix chain '8' and resid 83 through 87 removed outlier: 3.669A pdb=" N THR 8 87 " --> pdb=" O PRO 8 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.521A pdb=" N GLY A 516 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 517 " --> pdb=" O GLY A 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 517' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 570 through 595 removed outlier: 3.702A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.490A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.537A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 661 Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.573A pdb=" N GLU B 62 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 115 removed outlier: 3.633A pdb=" N HIS B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.653A pdb=" N LEU B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 126' Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.845A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 387 through 390 removed outlier: 3.807A pdb=" N LEU B 390 " --> pdb=" O THR B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'C' and resid 100D through 100H removed outlier: 3.916A pdb=" N PHE C 100G" --> pdb=" O VAL C 100D" (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'F' and resid 61 through 64 removed outlier: 4.073A pdb=" N GLN F 64 " --> pdb=" O ARG F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.713A pdb=" N THR F 87 " --> pdb=" O PRO F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 517 removed outlier: 3.521A pdb=" N GLY G 516 " --> pdb=" O VAL G 513 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA G 517 " --> pdb=" O GLY G 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 513 through 517' Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 570 through 595 removed outlier: 3.729A pdb=" N LYS G 574 " --> pdb=" O VAL G 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 removed outlier: 3.710A pdb=" N TRP G 614 " --> pdb=" O ASN G 611 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER G 615 " --> pdb=" O SER G 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 611 through 615' Processing helix chain 'G' and resid 619 through 624 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 641 through 661 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.692A pdb=" N GLN H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.084A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.646A pdb=" N GLN I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.024A pdb=" N ASP I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR I 87 " --> pdb=" O ASP I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.145A pdb=" N ILE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 62 removed outlier: 3.587A pdb=" N GLU K 62 " --> pdb=" O LYS K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 115 removed outlier: 3.541A pdb=" N MET K 104 " --> pdb=" O MET K 100 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS K 105 " --> pdb=" O VAL K 101 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE K 109 " --> pdb=" O HIS K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 126 removed outlier: 4.006A pdb=" N CYS K 126 " --> pdb=" O THR K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 198 Processing helix chain 'K' and resid 335 through 350 Processing helix chain 'K' and resid 351 through 353 No H-bonds generated for 'chain 'K' and resid 351 through 353' Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.657A pdb=" N THR K 372 " --> pdb=" O ASP K 368 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR K 373 " --> pdb=" O LEU K 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 368 through 373' Processing helix chain 'K' and resid 387 through 390 removed outlier: 3.821A pdb=" N LEU K 390 " --> pdb=" O THR K 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 387 through 390' Processing helix chain 'K' and resid 475 through 479 removed outlier: 3.534A pdb=" N ASN K 478 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.213A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100D through 100H removed outlier: 3.984A pdb=" N PHE M 100G" --> pdb=" O VAL M 100D" (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'P' and resid 61 through 64 removed outlier: 4.123A pdb=" N GLN P 64 " --> pdb=" O ARG P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 64' Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.731A pdb=" N THR P 87 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 513 through 517 removed outlier: 3.545A pdb=" N GLY Q 516 " --> pdb=" O VAL Q 513 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA Q 517 " --> pdb=" O GLY Q 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 513 through 517' Processing helix chain 'Q' and resid 529 through 534 Processing helix chain 'Q' and resid 570 through 595 removed outlier: 3.728A pdb=" N LYS Q 574 " --> pdb=" O VAL Q 570 " (cutoff:3.500A) Processing helix chain 'Q' and resid 611 through 616 removed outlier: 4.362A pdb=" N SER Q 615 " --> pdb=" O ASN Q 611 " (cutoff:3.500A) Processing helix chain 'Q' and resid 619 through 624 Processing helix chain 'Q' and resid 627 through 635 Processing helix chain 'Q' and resid 641 through 661 Processing helix chain 'R' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLN R 64 " --> pdb=" O PRO R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 61 through 64' Processing helix chain 'R' and resid 83 through 87 removed outlier: 3.971A pdb=" N ASP R 86 " --> pdb=" O THR R 83 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR R 87 " --> pdb=" O ASP R 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 83 through 87' Processing helix chain 'S' and resid 79 through 83 removed outlier: 4.184A pdb=" N ILE S 83 " --> pdb=" O PRO S 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 495 through 499 removed outlier: 6.045A pdb=" N VAL 2 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 606 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A 604 " --> pdb=" O VAL 2 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 45 through 47 removed outlier: 4.022A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain '2' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain '2' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain '2' and resid 202 through 203 removed outlier: 7.002A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 260 through 261 removed outlier: 7.883A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 11.652A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 11.755A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 12.160A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 271 through 273 removed outlier: 10.998A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 12.160A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 11.755A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 11.652A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain '2' and resid 359 through 361 removed outlier: 3.647A pdb=" N ILE 2 359 " --> pdb=" O TRP 2 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER 2 393 " --> pdb=" O PHE 2 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '5' and resid 11 through 12 removed outlier: 3.834A pdb=" N VAL 5 12 " --> pdb=" O THR 5 108 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR 5 33 " --> pdb=" O THR 5 95 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP 5 34 " --> pdb=" O TYR 5 50 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR 5 50 " --> pdb=" O TRP 5 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP 5 36 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '5' and resid 17 through 22 Processing sheet with id=AB4, first strand: chain '5' and resid 99 through 100A Processing sheet with id=AB5, first strand: chain '6' and resid 9 through 13 removed outlier: 3.689A pdb=" N THR 6 102 " --> pdb=" O TYR 6 86 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLN 6 37 " --> pdb=" O LEU 6 46 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU 6 46 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '6' and resid 18 through 23 removed outlier: 3.643A pdb=" N CYS 6 23 " --> pdb=" O ALA 6 71 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA 6 71 " --> pdb=" O CYS 6 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '7' and resid 10 through 13 removed outlier: 6.407A pdb=" N TRP 7 34 " --> pdb=" O LEU 7 46 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG 7 44 " --> pdb=" O GLN 7 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '7' and resid 19 through 24 Processing sheet with id=AB9, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain '8' and resid 10 through 11 removed outlier: 6.648A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG 8 38 " --> pdb=" O TRP 8 47 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N TRP 8 47 " --> pdb=" O ARG 8 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '8' and resid 10 through 11 removed outlier: 6.648A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR 8 102 " --> pdb=" O ARG 8 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 495 through 499 removed outlier: 6.009A pdb=" N VAL B 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR G 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS G 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.067A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'B' and resid 202 through 203 removed outlier: 7.019A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 424 " --> pdb=" O MET B 434 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 260 through 261 removed outlier: 7.650A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.895A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 12.171A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 271 through 273 removed outlier: 11.041A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.171A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.895A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.825A pdb=" N VAL C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR C 33 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR C 50 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 17 through 22 Processing sheet with id=AD4, first strand: chain 'C' and resid 100 through 100A Processing sheet with id=AD5, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.739A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 84 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.557A pdb=" N CYS D 23 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 13 removed outlier: 5.678A pdb=" N GLN E 36 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU E 45 " --> pdb=" O GLN E 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AD9, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.667A pdb=" N VAL F 10 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.667A pdb=" N VAL F 10 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.773A pdb=" N TYR H 58 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.773A pdb=" N TYR H 58 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.891A pdb=" N TYR I 58 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY I 50 " --> pdb=" O TYR I 58 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.891A pdb=" N TYR I 58 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY I 50 " --> pdb=" O TYR I 58 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.935A pdb=" N THR J 53 " --> pdb=" O HIS J 49 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS J 49 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N HIS J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU J 33 " --> pdb=" O HIS J 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 495 through 499 removed outlier: 6.061A pdb=" N VAL K 36 " --> pdb=" O THR Q 606 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR Q 606 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS Q 604 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 45 through 47 removed outlier: 4.112A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 91 through 93 Processing sheet with id=AF5, first strand: chain 'K' and resid 169 through 177 Processing sheet with id=AF6, first strand: chain 'K' and resid 202 through 203 removed outlier: 7.045A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 260 through 261 removed outlier: 7.471A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 11.640A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE K 453 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 12.065A pdb=" N PHE K 288 " --> pdb=" O ILE K 453 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER K 334 " --> pdb=" O GLN K 293 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 271 through 273 removed outlier: 11.011A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 12.065A pdb=" N PHE K 288 " --> pdb=" O ILE K 453 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE K 453 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 11.640A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AG1, first strand: chain 'K' and resid 359 through 361 removed outlier: 3.646A pdb=" N ILE K 359 " --> pdb=" O TRP K 395 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER K 393 " --> pdb=" O PHE K 361 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.961A pdb=" N THR L 53 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.743A pdb=" N VAL M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.743A pdb=" N VAL M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS M 96 " --> pdb=" O TYR M 100O" (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY M 98 " --> pdb=" O TYR M 100M" (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR M 100M" --> pdb=" O GLY M 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 17 through 22 Processing sheet with id=AG7, first strand: chain 'N' and resid 9 through 13 removed outlier: 3.706A pdb=" N THR N 102 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.673A pdb=" N CYS N 23 " --> pdb=" O ALA N 71 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 10 through 13 removed outlier: 5.852A pdb=" N GLN O 36 " --> pdb=" O LEU O 45 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU O 45 " --> pdb=" O GLN O 36 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 19 through 24 Processing sheet with id=AH2, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AH3, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.702A pdb=" N VAL P 10 " --> pdb=" O VAL P 110 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.702A pdb=" N VAL P 10 " --> pdb=" O VAL P 110 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 3 through 7 Processing sheet with id=AH6, first strand: chain 'R' and resid 58 through 59 removed outlier: 3.833A pdb=" N TYR R 58 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY R 50 " --> pdb=" O TYR R 58 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 58 through 59 removed outlier: 3.833A pdb=" N TYR R 58 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY R 50 " --> pdb=" O TYR R 58 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AH9, first strand: chain 'S' and resid 53 through 54 removed outlier: 4.017A pdb=" N THR S 53 " --> pdb=" O HIS S 49 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS S 49 " --> pdb=" O THR S 53 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N HIS S 49 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU S 33 " --> pdb=" O HIS S 49 " (cutoff:3.500A) 1050 hydrogen bonds defined for protein. 2652 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: 7.64 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9656 1.34 - 1.46: 9036 1.46 - 1.59: 14218 1.59 - 1.71: 29 1.71 - 1.83: 229 Bond restraints: 33168 Sorted by residual: bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG y 1 " pdb=" O5 NAG y 1 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C1 MAN y 4 " pdb=" C2 MAN y 4 " ideal model delta sigma weight residual 1.526 1.646 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1 MAN i 4 " pdb=" C2 MAN i 4 " ideal model delta sigma weight residual 1.526 1.634 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C1 MANJA 4 " pdb=" C2 MANJA 4 " ideal model delta sigma weight residual 1.526 1.632 -0.106 2.00e-02 2.50e+03 2.79e+01 ... (remaining 33163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 43716 3.83 - 7.67: 1221 7.67 - 11.50: 123 11.50 - 15.34: 15 15.34 - 19.17: 6 Bond angle restraints: 45081 Sorted by residual: angle pdb=" C ILE 8 48 " pdb=" N GLY 8 49 " pdb=" CA GLY 8 49 " ideal model delta sigma weight residual 121.35 113.60 7.75 1.03e+00 9.43e-01 5.66e+01 angle pdb=" C ASP 7 49 " pdb=" N THR 7 50 " pdb=" CA THR 7 50 " ideal model delta sigma weight residual 121.54 135.61 -14.07 1.91e+00 2.74e-01 5.42e+01 angle pdb=" C ASP E 49 " pdb=" N THR E 50 " pdb=" CA THR E 50 " ideal model delta sigma weight residual 121.54 135.45 -13.91 1.91e+00 2.74e-01 5.31e+01 angle pdb=" C ASP O 49 " pdb=" N THR O 50 " pdb=" CA THR O 50 " ideal model delta sigma weight residual 121.54 135.44 -13.90 1.91e+00 2.74e-01 5.30e+01 angle pdb=" N VAL A 570 " pdb=" CA VAL A 570 " pdb=" C VAL A 570 " ideal model delta sigma weight residual 113.47 106.69 6.78 1.01e+00 9.80e-01 4.50e+01 ... (remaining 45076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 15615 17.68 - 35.35: 2121 35.35 - 53.02: 435 53.02 - 70.70: 81 70.70 - 88.37: 18 Dihedral angle restraints: 18270 sinusoidal: 7269 harmonic: 11001 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 -178.63 -88.37 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CA CYS B 201 " pdb=" C CYS B 201 " pdb=" N THR B 202 " pdb=" CA THR B 202 " ideal model delta harmonic sigma weight residual -180.00 -140.39 -39.61 0 5.00e+00 4.00e-02 6.28e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 162.40 -69.40 1 1.00e+01 1.00e-02 6.22e+01 ... (remaining 18267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 5168 0.157 - 0.314: 344 0.314 - 0.470: 29 0.470 - 0.627: 3 0.627 - 0.784: 3 Chirality restraints: 5547 Sorted by residual: chirality pdb=" C1 NAGJA 1 " pdb=" ND2 ASN K 276 " pdb=" C2 NAGJA 1 " pdb=" O5 NAGJA 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C1 NAG y 1 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG y 1 " pdb=" O5 NAG y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN 2 276 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 5544 not shown) Planarity restraints: 5526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE 8 100D" 0.081 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO 8 100E" -0.210 5.00e-02 4.00e+02 pdb=" CA PRO 8 100E" 0.063 5.00e-02 4.00e+02 pdb=" CD PRO 8 100E" 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE P 100D" 0.080 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO P 100E" -0.207 5.00e-02 4.00e+02 pdb=" CA PRO P 100E" 0.062 5.00e-02 4.00e+02 pdb=" CD PRO P 100E" 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 100D" -0.071 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO F 100E" 0.182 5.00e-02 4.00e+02 pdb=" CA PRO F 100E" -0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 100E" -0.058 5.00e-02 4.00e+02 ... (remaining 5523 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9960 2.81 - 3.33: 26013 3.33 - 3.86: 54732 3.86 - 4.38: 55599 4.38 - 4.90: 96473 Nonbonded interactions: 242777 Sorted by model distance: nonbonded pdb=" O ASP A 632 " pdb=" OG SER A 636 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP 5 56 " pdb=" O2 BMA V 3 " model vdw 2.301 3.040 nonbonded pdb=" OD1 ASP C 56 " pdb=" O2 BMA l 3 " model vdw 2.302 3.040 nonbonded pdb=" OD1 ASP M 56 " pdb=" O2 BMA 1 3 " model vdw 2.306 3.040 nonbonded pdb=" OG SER K 334 " pdb=" OG1 THR K 337 " model vdw 2.307 3.040 ... (remaining 242772 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: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'AA' selection = chain 'CA' selection = chain 'DA' selection = chain 'GA' selection = chain 'IA' selection = chain 'U' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'h' selection = chain 'k' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain '1' selection = chain '9' selection = chain 'JA' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '2' selection = chain 'B' selection = chain 'K' } ncs_group { reference = chain '3' selection = chain 'FA' selection = chain 'W' selection = chain 'e' selection = chain 'm' selection = chain 'u' } ncs_group { reference = chain '4' selection = chain 'EA' selection = chain 'X' selection = chain 'd' selection = chain 'n' selection = chain 't' } ncs_group { reference = chain '5' selection = chain 'C' selection = chain 'M' } ncs_group { reference = chain '6' selection = chain 'D' selection = chain 'N' } ncs_group { reference = chain '7' selection = chain 'E' selection = chain 'O' } ncs_group { reference = chain '8' selection = chain 'F' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'Q' } ncs_group { reference = chain 'BA' selection = chain 'a' selection = chain 'q' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'HA' selection = chain 'g' selection = chain 'w' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'S' } 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 group one per residue 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 32.040 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.014 0.140 33405 Z= 0.665 Angle : 1.606 19.169 45741 Z= 0.807 Chirality : 0.087 0.784 5547 Planarity : 0.010 0.121 5469 Dihedral : 16.074 86.554 11073 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 2.64 % Allowed : 17.57 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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 are not related in a simple way. whole: -3.58 (0.11), residues: 3768 helix: -4.26 (0.12), residues: 396 sheet: -1.27 (0.14), residues: 1188 loop : -2.75 (0.11), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 8 61 TYR 0.035 0.004 TYR F 59 PHE 0.047 0.006 PHE 2 288 TRP 0.038 0.004 TRP 8 50 HIS 0.015 0.003 HIS H 100 Details of bonding type rmsd/Z covalent geometry : bond 0.01439 / 0.66 (33168) covalent geometry : angle 1.52363 / 0.79 (45081) SS BOND : bond 0.01102 / 0.68 ( 51) SS BOND : angle 3.81195 / 2.48 ( 102) hydrogen bonds : bond 0.14380 / 9.71 ( 976) hydrogen bonds : angle 7.68635 / 5.28 ( 2652) link_ALPHA1-2 : bond 0.00689 / 0.44 ( 9) link_ALPHA1-2 : angle 2.49075 / 1.46 ( 27) link_ALPHA1-3 : bond 0.01367 / 0.90 ( 24) link_ALPHA1-3 : angle 3.52516 / 2.41 ( 72) link_ALPHA1-6 : bond 0.01175 / 0.73 ( 18) link_ALPHA1-6 : angle 2.10318 / 1.29 ( 54) link_BETA1-4 : bond 0.01346 / 0.86 ( 78) link_BETA1-4 : angle 4.93681 / 3.25 ( 234) link_NAG-ASN : bond 0.01971 / 1.26 ( 57) link_NAG-ASN : angle 5.35792 / 3.65 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 605 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 2 271 MET cc_start: 0.8001 (mtm) cc_final: 0.7789 (mtm) REVERT: 2 504 ARG cc_start: 0.8076 (mtm180) cc_final: 0.7760 (ttp-110) REVERT: 5 44 GLN cc_start: 0.8772 (pm20) cc_final: 0.8552 (pm20) REVERT: 5 103 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8440 (mtmm) REVERT: 6 28 LEU cc_start: 0.8987 (mt) cc_final: 0.8772 (mt) REVERT: 6 42 GLN cc_start: 0.8730 (mt0) cc_final: 0.8488 (mp10) REVERT: 7 17 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8417 (mp0) REVERT: A 530 MET cc_start: 0.8087 (mtm) cc_final: 0.7213 (mtm) REVERT: A 584 GLU cc_start: 0.7869 (tt0) cc_final: 0.7593 (tt0) REVERT: B 261 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9024 (pp) REVERT: B 289 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8616 (p0) REVERT: B 479 TRP cc_start: 0.8596 (m-10) cc_final: 0.8242 (m-90) REVERT: C 44 GLN cc_start: 0.8541 (pm20) cc_final: 0.8319 (pm20) REVERT: D 70 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8105 (m) REVERT: G 530 MET cc_start: 0.8552 (mtm) cc_final: 0.7713 (mtm) REVERT: G 571 TRP cc_start: 0.8531 (m100) cc_final: 0.8303 (m-10) REVERT: H 4 LEU cc_start: 0.8917 (mm) cc_final: 0.8667 (mt) REVERT: H 12 MET cc_start: 0.7053 (mtp) cc_final: 0.6071 (ttm) REVERT: H 20 LEU cc_start: 0.7071 (mt) cc_final: 0.6780 (mt) REVERT: H 48 ILE cc_start: 0.7379 (mt) cc_final: 0.7115 (mp) REVERT: H 52 TYR cc_start: 0.7104 (m-80) cc_final: 0.6833 (m-80) REVERT: I 4 LEU cc_start: 0.8686 (mt) cc_final: 0.8281 (mm) REVERT: I 12 MET cc_start: 0.6146 (mtp) cc_final: 0.5600 (ttm) REVERT: I 20 LEU cc_start: 0.7065 (mt) cc_final: 0.6607 (mt) REVERT: I 52 TYR cc_start: 0.7654 (m-80) cc_final: 0.7140 (m-80) REVERT: J 5 THR cc_start: 0.6959 (m) cc_final: 0.6665 (m) REVERT: J 30 LYS cc_start: 0.7642 (ttmm) cc_final: 0.7431 (mtmt) REVERT: J 59 PRO cc_start: 0.8367 (Cg_exo) cc_final: 0.7696 (Cg_endo) REVERT: K 427 TRP cc_start: 0.8763 (m-90) cc_final: 0.8132 (m-90) REVERT: L 5 THR cc_start: 0.7110 (m) cc_final: 0.6208 (m) REVERT: L 59 PRO cc_start: 0.8344 (Cg_exo) cc_final: 0.7694 (Cg_endo) REVERT: M 75 LYS cc_start: 0.8749 (mttt) cc_final: 0.8482 (mtpt) REVERT: N 104 LEU cc_start: 0.9031 (mm) cc_final: 0.8712 (tp) REVERT: O 59 ASP cc_start: 0.8571 (p0) cc_final: 0.8282 (t0) REVERT: P 59 TYR cc_start: 0.8369 (m-80) cc_final: 0.6724 (m-10) REVERT: P 102 TYR cc_start: 0.6789 (m-80) cc_final: 0.6548 (m-80) REVERT: Q 530 MET cc_start: 0.8474 (mtt) cc_final: 0.7762 (mtt) REVERT: R 4 LEU cc_start: 0.8426 (mt) cc_final: 0.7828 (mm) REVERT: R 36 TRP cc_start: 0.7810 (m100) cc_final: 0.7204 (m100) REVERT: R 52 TYR cc_start: 0.7154 (m-80) cc_final: 0.6871 (m-80) REVERT: R 102 LEU cc_start: 0.8026 (mt) cc_final: 0.7755 (mt) REVERT: S 5 THR cc_start: 0.7198 (m) cc_final: 0.6299 (m) REVERT: S 59 PRO cc_start: 0.8104 (Cg_exo) cc_final: 0.7507 (Cg_endo) outliers start: 88 outliers final: 46 residues processed: 684 average time/residue: 0.2354 time to fit residues: 250.2195 Evaluate side-chains 445 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 396 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 66 HIS 2 94 ASN ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 287 GLN 2 302 ASN 2 348 GLN 2 352 HIS 8 6 GLN 8 64 GLN 8 101 GLN A 577 GLN B 66 HIS B 94 ASN B 99 ASN B 287 GLN B 348 GLN B 374 HIS ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN H 77 HIS J 6 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS K 94 ASN K 99 ASN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 GLN K 287 GLN K 348 GLN L 49 HIS P 6 GLN P 64 GLN Q 577 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 49 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.079338 restraints weight = 96053.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.078880 restraints weight = 71733.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079256 restraints weight = 64310.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080026 restraints weight = 56155.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080106 restraints weight = 50324.717| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33405 Z= 0.174 Angle : 0.881 13.932 45741 Z= 0.419 Chirality : 0.049 0.386 5547 Planarity : 0.007 0.098 5469 Dihedral : 6.984 34.661 4152 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.33 % Allowed : 5.26 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 are not related in a simple way. whole: -2.71 (0.12), residues: 3768 helix: -2.27 (0.22), residues: 396 sheet: -0.97 (0.14), residues: 1173 loop : -2.26 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 8 94 TYR 0.023 0.002 TYR F 102 PHE 0.030 0.002 PHE 8 100D TRP 0.026 0.002 TRP F 100F HIS 0.012 0.002 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (33168) covalent geometry : angle 0.82853 / 0.41 (45081) SS BOND : bond 0.00582 / 0.35 ( 51) SS BOND : angle 2.50516 / 1.55 ( 102) hydrogen bonds : bond 0.04393 / 2.91 ( 976) hydrogen bonds : angle 6.32813 / 4.37 ( 2652) link_ALPHA1-2 : bond 0.00254 / 0.16 ( 9) link_ALPHA1-2 : angle 2.14741 / 1.29 ( 27) link_ALPHA1-3 : bond 0.00870 / 0.53 ( 24) link_ALPHA1-3 : angle 2.04708 / 1.44 ( 72) link_ALPHA1-6 : bond 0.00670 / 0.39 ( 18) link_ALPHA1-6 : angle 1.57856 / 1.04 ( 54) link_BETA1-4 : bond 0.00619 / 0.38 ( 78) link_BETA1-4 : angle 2.63424 / 1.76 ( 234) link_NAG-ASN : bond 0.00501 / 0.31 ( 57) link_NAG-ASN : angle 3.21382 / 2.20 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 553 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 504 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7535 (ttp-110) REVERT: 5 44 GLN cc_start: 0.8709 (pm20) cc_final: 0.8501 (pm20) REVERT: 5 100 MET cc_start: 0.8939 (mpp) cc_final: 0.8488 (mmp) REVERT: 6 42 GLN cc_start: 0.8742 (mt0) cc_final: 0.8527 (mp10) REVERT: 7 89 GLN cc_start: 0.7663 (pm20) cc_final: 0.7040 (pm20) REVERT: 8 51 ILE cc_start: 0.9124 (tt) cc_final: 0.8742 (mp) REVERT: 8 59 TYR cc_start: 0.7653 (m-80) cc_final: 0.7357 (m-80) REVERT: 8 75 GLN cc_start: 0.8775 (mp10) cc_final: 0.8558 (pm20) REVERT: 8 81 GLU cc_start: 0.7965 (pt0) cc_final: 0.7731 (pm20) REVERT: 8 82 LEU cc_start: 0.9339 (mt) cc_final: 0.8976 (mt) REVERT: A 530 MET cc_start: 0.8119 (mtm) cc_final: 0.7249 (mtm) REVERT: A 591 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8894 (tm-30) REVERT: A 619 LEU cc_start: 0.9293 (pp) cc_final: 0.9023 (tt) REVERT: B 99 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8497 (t0) REVERT: B 475 MET cc_start: 0.7907 (mmt) cc_final: 0.7598 (mmt) REVERT: C 44 GLN cc_start: 0.8621 (pm20) cc_final: 0.8402 (pm20) REVERT: C 100 MET cc_start: 0.8795 (mpp) cc_final: 0.8327 (mmp) REVERT: E 89 GLN cc_start: 0.7987 (pm20) cc_final: 0.7650 (pm20) REVERT: F 75 GLN cc_start: 0.8705 (mp10) cc_final: 0.8432 (pm20) REVERT: G 530 MET cc_start: 0.8639 (mtm) cc_final: 0.7634 (mtm) REVERT: G 571 TRP cc_start: 0.8501 (m100) cc_final: 0.8208 (m-10) REVERT: G 584 GLU cc_start: 0.7952 (tt0) cc_final: 0.7548 (tm-30) REVERT: G 591 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8713 (tm-30) REVERT: H 4 LEU cc_start: 0.9026 (mm) cc_final: 0.8780 (mm) REVERT: H 12 MET cc_start: 0.6554 (mtp) cc_final: 0.6156 (ttp) REVERT: H 46 GLU cc_start: 0.8459 (tp30) cc_final: 0.7973 (tp30) REVERT: I 46 GLU cc_start: 0.8277 (tp30) cc_final: 0.7896 (tp30) REVERT: I 52 TYR cc_start: 0.7594 (m-80) cc_final: 0.7332 (m-80) REVERT: I 77 HIS cc_start: 0.6631 (m-70) cc_final: 0.6349 (m90) REVERT: J 5 THR cc_start: 0.6721 (m) cc_final: 0.6152 (m) REVERT: K 479 TRP cc_start: 0.8382 (m-90) cc_final: 0.8125 (m-90) REVERT: M 75 LYS cc_start: 0.8755 (mttt) cc_final: 0.8469 (mmmt) REVERT: O 89 GLN cc_start: 0.7716 (pm20) cc_final: 0.7307 (pm20) REVERT: P 51 ILE cc_start: 0.9150 (tt) cc_final: 0.8923 (mp) REVERT: P 59 TYR cc_start: 0.7809 (m-80) cc_final: 0.6166 (m-10) REVERT: P 102 TYR cc_start: 0.6838 (m-80) cc_final: 0.6564 (m-80) REVERT: Q 530 MET cc_start: 0.8598 (mtm) cc_final: 0.7940 (mtt) REVERT: Q 619 LEU cc_start: 0.9370 (pp) cc_final: 0.9088 (tt) REVERT: Q 638 TYR cc_start: 0.8151 (m-80) cc_final: 0.7538 (m-10) REVERT: R 4 LEU cc_start: 0.8629 (mt) cc_final: 0.8275 (mm) REVERT: R 36 TRP cc_start: 0.7874 (m100) cc_final: 0.7624 (m100) REVERT: R 46 GLU cc_start: 0.8334 (tp30) cc_final: 0.7695 (tp30) REVERT: S 45 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7831 (tpp80) REVERT: S 70 GLU cc_start: 0.7465 (tp30) cc_final: 0.7253 (tp30) outliers start: 11 outliers final: 2 residues processed: 564 average time/residue: 0.2233 time to fit residues: 199.7821 Evaluate side-chains 389 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 386 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 280 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 354 optimal weight: 30.0000 chunk 236 optimal weight: 3.9990 chunk 157 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 99 ASN 5 32 ASN B 66 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 38 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 352 HIS M 32 ASN P 6 GLN R 100 HIS S 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.077847 restraints weight = 95852.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078110 restraints weight = 71393.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.078824 restraints weight = 57207.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079184 restraints weight = 52685.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079227 restraints weight = 48188.178| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 33405 Z= 0.213 Angle : 0.875 16.070 45741 Z= 0.411 Chirality : 0.048 0.238 5547 Planarity : 0.006 0.091 5469 Dihedral : 6.604 32.474 4152 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.24 % Allowed : 5.08 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: -2.43 (0.13), residues: 3768 helix: -1.39 (0.25), residues: 393 sheet: -0.92 (0.14), residues: 1233 loop : -2.13 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 61 TYR 0.021 0.002 TYR J 36 PHE 0.030 0.002 PHE F 100D TRP 0.027 0.002 TRP 8 100F HIS 0.008 0.001 HIS 2 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (33168) covalent geometry : angle 0.81913 / 0.40 (45081) SS BOND : bond 0.00596 / 0.38 ( 51) SS BOND : angle 2.54486 / 1.61 ( 102) hydrogen bonds : bond 0.04399 / 2.93 ( 976) hydrogen bonds : angle 5.94236 / 4.08 ( 2652) link_ALPHA1-2 : bond 0.00298 / 0.18 ( 9) link_ALPHA1-2 : angle 1.82837 / 1.11 ( 27) link_ALPHA1-3 : bond 0.00859 / 0.54 ( 24) link_ALPHA1-3 : angle 2.09177 / 1.44 ( 72) link_ALPHA1-6 : bond 0.00623 / 0.36 ( 18) link_ALPHA1-6 : angle 1.72412 / 1.10 ( 54) link_BETA1-4 : bond 0.00703 / 0.44 ( 78) link_BETA1-4 : angle 2.56051 / 1.69 ( 234) link_NAG-ASN : bond 0.00566 / 0.37 ( 57) link_NAG-ASN : angle 3.39821 / 2.34 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 503 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 271 MET cc_start: 0.7692 (mtm) cc_final: 0.7435 (mtm) REVERT: 2 377 ASN cc_start: 0.8522 (t0) cc_final: 0.8200 (t0) REVERT: 5 13 LYS cc_start: 0.7824 (pttp) cc_final: 0.7431 (tppt) REVERT: 5 34 TRP cc_start: 0.8145 (m100) cc_final: 0.7906 (m100) REVERT: 7 79 ARG cc_start: 0.7026 (mpt180) cc_final: 0.6777 (mpt180) REVERT: 7 89 GLN cc_start: 0.7587 (pm20) cc_final: 0.7067 (pm20) REVERT: 8 51 ILE cc_start: 0.9220 (tt) cc_final: 0.8761 (mp) REVERT: 8 82 LEU cc_start: 0.9433 (mt) cc_final: 0.9069 (mt) REVERT: A 530 MET cc_start: 0.8116 (mtm) cc_final: 0.7561 (mtm) REVERT: A 619 LEU cc_start: 0.9294 (pp) cc_final: 0.8993 (tt) REVERT: B 122 LEU cc_start: 0.9581 (mt) cc_final: 0.9344 (mm) REVERT: B 377 ASN cc_start: 0.8428 (t0) cc_final: 0.8173 (t0) REVERT: C 44 GLN cc_start: 0.8587 (pm20) cc_final: 0.8378 (pm20) REVERT: C 100 MET cc_start: 0.8868 (mpp) cc_final: 0.8520 (mmp) REVERT: E 13 LEU cc_start: 0.8561 (mt) cc_final: 0.8343 (mt) REVERT: E 70 PHE cc_start: 0.8190 (m-80) cc_final: 0.7900 (m-10) REVERT: E 89 GLN cc_start: 0.7720 (pm20) cc_final: 0.7511 (pm20) REVERT: G 530 MET cc_start: 0.8574 (mtm) cc_final: 0.7574 (mtm) REVERT: G 571 TRP cc_start: 0.8412 (m100) cc_final: 0.8170 (m-10) REVERT: G 591 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8693 (tm-30) REVERT: H 12 MET cc_start: 0.6828 (mtp) cc_final: 0.6461 (ttp) REVERT: H 46 GLU cc_start: 0.8425 (tp30) cc_final: 0.7845 (tp30) REVERT: I 16 GLU cc_start: 0.4812 (mm-30) cc_final: 0.4539 (mm-30) REVERT: I 46 GLU cc_start: 0.8316 (tp30) cc_final: 0.7849 (tp30) REVERT: J 4 MET cc_start: 0.7681 (tpt) cc_final: 0.7338 (tpt) REVERT: J 88 CYS cc_start: 0.4980 (p) cc_final: 0.4018 (p) REVERT: K 104 MET cc_start: 0.8470 (ttm) cc_final: 0.8063 (ttm) REVERT: K 479 TRP cc_start: 0.8487 (m-90) cc_final: 0.8144 (m-90) REVERT: K 484 TYR cc_start: 0.9069 (p90) cc_final: 0.8757 (p90) REVERT: M 34 TRP cc_start: 0.8127 (m100) cc_final: 0.7824 (m100) REVERT: M 75 LYS cc_start: 0.8699 (mttt) cc_final: 0.8436 (mmmt) REVERT: M 100 MET cc_start: 0.8813 (mpp) cc_final: 0.8169 (mmt) REVERT: P 59 TYR cc_start: 0.7975 (m-80) cc_final: 0.6663 (m-80) REVERT: P 102 TYR cc_start: 0.6800 (m-80) cc_final: 0.6516 (m-80) REVERT: Q 530 MET cc_start: 0.8550 (mtm) cc_final: 0.7968 (mtt) REVERT: Q 619 LEU cc_start: 0.9375 (pp) cc_final: 0.9039 (tt) REVERT: Q 638 TYR cc_start: 0.8213 (m-80) cc_final: 0.7395 (m-10) REVERT: R 46 GLU cc_start: 0.8326 (tp30) cc_final: 0.7769 (tp30) REVERT: S 6 GLN cc_start: 0.6600 (mt0) cc_final: 0.6347 (mt0) outliers start: 8 outliers final: 6 residues processed: 510 average time/residue: 0.2093 time to fit residues: 172.1324 Evaluate side-chains 382 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 376 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 309 optimal weight: 20.0000 chunk 240 optimal weight: 6.9990 chunk 328 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 350 optimal weight: 0.0070 chunk 285 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 chunk 301 optimal weight: 9.9990 chunk 347 optimal weight: 0.8980 overall best weight: 2.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 203 GLN 2 348 GLN 8 6 GLN B 66 HIS F 64 GLN F 101 GLN ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.103557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.078867 restraints weight = 95461.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078907 restraints weight = 73051.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.079470 restraints weight = 58480.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.079804 restraints weight = 57593.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.079995 restraints weight = 50096.730| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33405 Z= 0.167 Angle : 0.816 13.561 45741 Z= 0.384 Chirality : 0.047 0.224 5547 Planarity : 0.005 0.088 5469 Dihedral : 6.194 33.801 4152 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 are not related in a simple way. whole: -2.12 (0.13), residues: 3768 helix: -0.68 (0.27), residues: 378 sheet: -0.79 (0.15), residues: 1137 loop : -1.94 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 TYR 0.021 0.001 TYR F 102 PHE 0.018 0.002 PHE O 70 TRP 0.036 0.002 TRP 8 100F HIS 0.007 0.001 HIS 2 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (33168) covalent geometry : angle 0.76881 / 0.37 (45081) SS BOND : bond 0.00683 / 0.42 ( 51) SS BOND : angle 2.39287 / 1.51 ( 102) hydrogen bonds : bond 0.04008 / 2.67 ( 976) hydrogen bonds : angle 5.64554 / 3.88 ( 2652) link_ALPHA1-2 : bond 0.00313 / 0.19 ( 9) link_ALPHA1-2 : angle 1.72618 / 1.07 ( 27) link_ALPHA1-3 : bond 0.00779 / 0.49 ( 24) link_ALPHA1-3 : angle 1.88487 / 1.31 ( 72) link_ALPHA1-6 : bond 0.00537 / 0.31 ( 18) link_ALPHA1-6 : angle 1.62482 / 1.05 ( 54) link_BETA1-4 : bond 0.00605 / 0.37 ( 78) link_BETA1-4 : angle 2.37741 / 1.57 ( 234) link_NAG-ASN : bond 0.00455 / 0.29 ( 57) link_NAG-ASN : angle 2.92272 / 2.00 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 501 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 100 MET cc_start: 0.8039 (ptm) cc_final: 0.7555 (ttm) REVERT: 2 271 MET cc_start: 0.7561 (mtm) cc_final: 0.7331 (mtm) REVERT: 2 377 ASN cc_start: 0.8442 (t0) cc_final: 0.8152 (t0) REVERT: 2 504 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7530 (ttp-110) REVERT: 5 100 ASP cc_start: 0.8788 (p0) cc_final: 0.8585 (p0) REVERT: 7 89 GLN cc_start: 0.7520 (pm20) cc_final: 0.7111 (pm20) REVERT: 8 59 TYR cc_start: 0.7840 (m-80) cc_final: 0.6563 (m-80) REVERT: 8 81 GLU cc_start: 0.8077 (pm20) cc_final: 0.7416 (pm20) REVERT: 8 82 LEU cc_start: 0.9257 (mt) cc_final: 0.8877 (mt) REVERT: A 530 MET cc_start: 0.8137 (mtm) cc_final: 0.7503 (mtt) REVERT: A 591 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8695 (tm-30) REVERT: A 595 ILE cc_start: 0.9341 (pt) cc_final: 0.8738 (mm) REVERT: A 619 LEU cc_start: 0.9268 (pp) cc_final: 0.8933 (tt) REVERT: A 658 GLN cc_start: 0.8670 (tt0) cc_final: 0.7325 (tp40) REVERT: B 161 MET cc_start: 0.9099 (tpp) cc_final: 0.8862 (tpp) REVERT: B 377 ASN cc_start: 0.8506 (t0) cc_final: 0.8287 (t0) REVERT: C 44 GLN cc_start: 0.8650 (pm20) cc_final: 0.8417 (pm20) REVERT: C 100 TYR cc_start: 0.8798 (p90) cc_final: 0.8481 (p90) REVERT: C 100 ASP cc_start: 0.8770 (p0) cc_final: 0.8538 (p0) REVERT: E 89 GLN cc_start: 0.7667 (pm20) cc_final: 0.7436 (pm20) REVERT: F 59 TYR cc_start: 0.7313 (m-80) cc_final: 0.6773 (m-80) REVERT: G 530 MET cc_start: 0.8461 (mtm) cc_final: 0.7627 (mtm) REVERT: G 571 TRP cc_start: 0.8399 (m100) cc_final: 0.8118 (m-10) REVERT: G 591 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8728 (tm-30) REVERT: H 12 MET cc_start: 0.6864 (mtp) cc_final: 0.6531 (ttp) REVERT: H 21 ILE cc_start: 0.7254 (mm) cc_final: 0.7034 (mm) REVERT: H 46 GLU cc_start: 0.8337 (tp30) cc_final: 0.7669 (tp30) REVERT: I 16 GLU cc_start: 0.4876 (mm-30) cc_final: 0.4645 (mm-30) REVERT: I 45 LEU cc_start: 0.7525 (tp) cc_final: 0.7149 (tt) REVERT: I 46 GLU cc_start: 0.8309 (tp30) cc_final: 0.7734 (tp30) REVERT: J 48 MET cc_start: 0.6681 (ptm) cc_final: 0.5831 (ptm) REVERT: J 88 CYS cc_start: 0.4652 (p) cc_final: 0.3556 (p) REVERT: K 122 LEU cc_start: 0.9478 (mt) cc_final: 0.9168 (mm) REVERT: K 479 TRP cc_start: 0.8481 (m-90) cc_final: 0.8078 (m-90) REVERT: K 484 TYR cc_start: 0.9048 (p90) cc_final: 0.8816 (p90) REVERT: M 75 LYS cc_start: 0.8619 (mttt) cc_final: 0.8398 (mmmt) REVERT: O 70 PHE cc_start: 0.7754 (m-10) cc_final: 0.7516 (m-10) REVERT: P 51 ILE cc_start: 0.9258 (tt) cc_final: 0.9056 (mp) REVERT: P 102 TYR cc_start: 0.6936 (m-80) cc_final: 0.6617 (m-80) REVERT: Q 530 MET cc_start: 0.8471 (mtm) cc_final: 0.7832 (mtt) REVERT: Q 595 ILE cc_start: 0.9227 (pt) cc_final: 0.8845 (mm) REVERT: Q 619 LEU cc_start: 0.9362 (pp) cc_final: 0.9013 (tt) REVERT: Q 638 TYR cc_start: 0.8204 (m-80) cc_final: 0.7538 (m-10) REVERT: R 46 GLU cc_start: 0.8320 (tp30) cc_final: 0.7885 (tp30) outliers start: 1 outliers final: 0 residues processed: 502 average time/residue: 0.2039 time to fit residues: 165.9315 Evaluate side-chains 383 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 119 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 208 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 287 GLN 2 478 ASN 6 52 ASN B 66 HIS B 103 GLN C 32 ASN F 6 GLN ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 GLN K 374 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.075459 restraints weight = 97272.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075400 restraints weight = 73773.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.075961 restraints weight = 62395.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.076368 restraints weight = 58416.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.076404 restraints weight = 53173.423| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 33405 Z= 0.288 Angle : 0.926 14.958 45741 Z= 0.434 Chirality : 0.049 0.247 5547 Planarity : 0.006 0.089 5469 Dihedral : 6.377 32.795 4152 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -2.12 (0.13), residues: 3768 helix: -0.27 (0.28), residues: 363 sheet: -0.71 (0.15), residues: 1155 loop : -2.06 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.023 0.002 TYR 2 484 PHE 0.024 0.003 PHE E 71 TRP 0.045 0.002 TRP F 36 HIS 0.008 0.002 HIS 2 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.29 (33168) covalent geometry : angle 0.87435 / 0.42 (45081) SS BOND : bond 0.00615 / 0.38 ( 51) SS BOND : angle 2.80465 / 1.77 ( 102) hydrogen bonds : bond 0.04589 / 3.04 ( 976) hydrogen bonds : angle 5.69793 / 3.90 ( 2652) link_ALPHA1-2 : bond 0.00307 / 0.19 ( 9) link_ALPHA1-2 : angle 1.83192 / 1.10 ( 27) link_ALPHA1-3 : bond 0.00831 / 0.53 ( 24) link_ALPHA1-3 : angle 2.19156 / 1.50 ( 72) link_ALPHA1-6 : bond 0.00676 / 0.41 ( 18) link_ALPHA1-6 : angle 1.78348 / 1.12 ( 54) link_BETA1-4 : bond 0.00635 / 0.39 ( 78) link_BETA1-4 : angle 2.50377 / 1.64 ( 234) link_NAG-ASN : bond 0.00771 / 0.49 ( 57) link_NAG-ASN : angle 3.29034 / 2.24 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 464 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 100 MET cc_start: 0.8235 (ptm) cc_final: 0.7917 (ttm) REVERT: 2 103 GLN cc_start: 0.7817 (pp30) cc_final: 0.7468 (pp30) REVERT: 2 271 MET cc_start: 0.7682 (mtm) cc_final: 0.7445 (mtm) REVERT: 2 504 ARG cc_start: 0.8008 (ttp-170) cc_final: 0.7551 (ttp-110) REVERT: 5 34 TRP cc_start: 0.8309 (m100) cc_final: 0.8097 (m100) REVERT: 5 100 MET cc_start: 0.8899 (mpp) cc_final: 0.8611 (mpp) REVERT: 5 100 ASP cc_start: 0.8811 (p0) cc_final: 0.8609 (p0) REVERT: 7 89 GLN cc_start: 0.7599 (pm20) cc_final: 0.7140 (pm20) REVERT: 8 51 ILE cc_start: 0.9268 (tt) cc_final: 0.8925 (mp) REVERT: 8 81 GLU cc_start: 0.8167 (pm20) cc_final: 0.7383 (pm20) REVERT: 8 82 LEU cc_start: 0.9340 (mt) cc_final: 0.8931 (mt) REVERT: A 530 MET cc_start: 0.8192 (mtm) cc_final: 0.7609 (mtm) REVERT: A 591 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8954 (tm-30) REVERT: A 619 LEU cc_start: 0.9321 (pp) cc_final: 0.8970 (tt) REVERT: A 658 GLN cc_start: 0.8674 (tt0) cc_final: 0.7372 (tp40) REVERT: B 161 MET cc_start: 0.9106 (tpp) cc_final: 0.8865 (tpp) REVERT: B 426 MET cc_start: 0.8964 (ptm) cc_final: 0.8601 (ptm) REVERT: B 427 TRP cc_start: 0.9146 (m-90) cc_final: 0.8597 (m-90) REVERT: C 44 GLN cc_start: 0.8764 (pm20) cc_final: 0.8550 (pm20) REVERT: C 100 ASP cc_start: 0.8780 (p0) cc_final: 0.8547 (p0) REVERT: E 13 LEU cc_start: 0.8600 (mt) cc_final: 0.8387 (mt) REVERT: E 70 PHE cc_start: 0.8103 (m-10) cc_final: 0.7853 (m-10) REVERT: E 89 GLN cc_start: 0.8016 (pm20) cc_final: 0.7392 (pm20) REVERT: F 59 TYR cc_start: 0.7804 (m-80) cc_final: 0.7261 (m-80) REVERT: F 82 LEU cc_start: 0.9503 (mt) cc_final: 0.9185 (mt) REVERT: G 530 MET cc_start: 0.8483 (mtm) cc_final: 0.7518 (mtm) REVERT: H 12 MET cc_start: 0.7016 (mtp) cc_final: 0.6532 (ttt) REVERT: H 16 GLU cc_start: 0.4990 (mm-30) cc_final: 0.4650 (mm-30) REVERT: H 46 GLU cc_start: 0.8401 (tp30) cc_final: 0.7816 (tp30) REVERT: H 77 HIS cc_start: 0.6801 (m90) cc_final: 0.6547 (m90) REVERT: I 12 MET cc_start: 0.6927 (ttm) cc_final: 0.6699 (ttp) REVERT: I 16 GLU cc_start: 0.4926 (mm-30) cc_final: 0.4670 (mm-30) REVERT: I 46 GLU cc_start: 0.8393 (tp30) cc_final: 0.7843 (tp30) REVERT: J 88 CYS cc_start: 0.5188 (p) cc_final: 0.4691 (p) REVERT: K 100 MET cc_start: 0.8796 (ppp) cc_final: 0.8191 (ppp) REVERT: K 122 LEU cc_start: 0.9500 (mt) cc_final: 0.9231 (mm) REVERT: M 34 TRP cc_start: 0.8048 (m100) cc_final: 0.7807 (m100) REVERT: M 44 GLN cc_start: 0.8718 (pm20) cc_final: 0.8491 (pm20) REVERT: M 100 MET cc_start: 0.8754 (mpp) cc_final: 0.8203 (mmp) REVERT: M 100 ASP cc_start: 0.8826 (p0) cc_final: 0.8580 (p0) REVERT: O 70 PHE cc_start: 0.7922 (m-10) cc_final: 0.7623 (m-10) REVERT: O 86 TYR cc_start: 0.7610 (m-80) cc_final: 0.7354 (m-80) REVERT: Q 530 MET cc_start: 0.8705 (mtm) cc_final: 0.8089 (mtt) REVERT: Q 595 ILE cc_start: 0.9351 (pt) cc_final: 0.8874 (mm) REVERT: Q 619 LEU cc_start: 0.9342 (pp) cc_final: 0.8969 (tt) REVERT: Q 638 TYR cc_start: 0.8200 (m-80) cc_final: 0.7605 (m-10) REVERT: R 46 GLU cc_start: 0.8432 (tp30) cc_final: 0.7943 (tp30) REVERT: S 5 THR cc_start: 0.7203 (m) cc_final: 0.6858 (m) REVERT: S 18 ARG cc_start: 0.7176 (ttt-90) cc_final: 0.6559 (mtp85) REVERT: S 24 ARG cc_start: 0.8322 (tmm160) cc_final: 0.7987 (tmm160) outliers start: 3 outliers final: 1 residues processed: 467 average time/residue: 0.2063 time to fit residues: 156.4403 Evaluate side-chains 371 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 141 optimal weight: 6.9990 chunk 231 optimal weight: 40.0000 chunk 334 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 288 optimal weight: 30.0000 chunk 43 optimal weight: 0.8980 chunk 358 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 203 GLN 2 478 ASN 6 51 ASN 6 52 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 HIS S 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.102957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.078273 restraints weight = 95347.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.078530 restraints weight = 69758.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.078868 restraints weight = 56119.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.079191 restraints weight = 54362.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.079305 restraints weight = 49935.325| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 33405 Z= 0.176 Angle : 0.837 13.720 45741 Z= 0.391 Chirality : 0.048 0.406 5547 Planarity : 0.005 0.088 5469 Dihedral : 6.085 31.792 4152 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.92 (0.13), residues: 3768 helix: -0.26 (0.28), residues: 378 sheet: -0.54 (0.15), residues: 1176 loop : -1.95 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.020 0.001 TYR B 484 PHE 0.017 0.002 PHE 7 82 TRP 0.049 0.002 TRP F 36 HIS 0.012 0.001 HIS 8 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (33168) covalent geometry : angle 0.79036 / 0.38 (45081) SS BOND : bond 0.00600 / 0.41 ( 51) SS BOND : angle 2.26808 / 1.44 ( 102) hydrogen bonds : bond 0.04020 / 2.67 ( 976) hydrogen bonds : angle 5.51525 / 3.77 ( 2652) link_ALPHA1-2 : bond 0.00287 / 0.17 ( 9) link_ALPHA1-2 : angle 1.70153 / 1.05 ( 27) link_ALPHA1-3 : bond 0.00759 / 0.47 ( 24) link_ALPHA1-3 : angle 1.85869 / 1.28 ( 72) link_ALPHA1-6 : bond 0.00520 / 0.30 ( 18) link_ALPHA1-6 : angle 1.61517 / 1.04 ( 54) link_BETA1-4 : bond 0.00569 / 0.35 ( 78) link_BETA1-4 : angle 2.32061 / 1.52 ( 234) link_NAG-ASN : bond 0.00503 / 0.30 ( 57) link_NAG-ASN : angle 3.09255 / 2.16 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 500 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 271 MET cc_start: 0.7541 (mtm) cc_final: 0.7330 (mtm) REVERT: 2 377 ASN cc_start: 0.8555 (t0) cc_final: 0.8277 (t0) REVERT: 2 504 ARG cc_start: 0.7950 (ttp-170) cc_final: 0.7482 (ttp-110) REVERT: 5 100 MET cc_start: 0.8939 (mpp) cc_final: 0.8544 (mpp) REVERT: 5 100 ASP cc_start: 0.8781 (p0) cc_final: 0.8562 (p0) REVERT: 7 89 GLN cc_start: 0.7356 (pm20) cc_final: 0.7093 (pm20) REVERT: 8 51 ILE cc_start: 0.9181 (tt) cc_final: 0.8780 (mp) REVERT: 8 82 LEU cc_start: 0.9366 (mt) cc_final: 0.8934 (mt) REVERT: A 530 MET cc_start: 0.8166 (mtm) cc_final: 0.7436 (mtm) REVERT: A 591 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8968 (tm-30) REVERT: A 619 LEU cc_start: 0.9312 (pp) cc_final: 0.8986 (tt) REVERT: A 658 GLN cc_start: 0.8545 (tt0) cc_final: 0.7209 (tp40) REVERT: C 100 ASP cc_start: 0.8771 (p0) cc_final: 0.8516 (p0) REVERT: E 70 PHE cc_start: 0.8213 (m-80) cc_final: 0.7919 (m-10) REVERT: E 89 GLN cc_start: 0.7771 (pm20) cc_final: 0.7089 (pm20) REVERT: F 59 TYR cc_start: 0.7656 (m-80) cc_final: 0.6838 (m-80) REVERT: F 82 LEU cc_start: 0.9397 (mt) cc_final: 0.9134 (mt) REVERT: G 530 MET cc_start: 0.8485 (mtm) cc_final: 0.7336 (mtm) REVERT: G 591 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8875 (tm-30) REVERT: H 12 MET cc_start: 0.6936 (mtp) cc_final: 0.6708 (ttp) REVERT: H 46 GLU cc_start: 0.8396 (tp30) cc_final: 0.7778 (tp30) REVERT: H 77 HIS cc_start: 0.6791 (m90) cc_final: 0.6509 (m90) REVERT: I 16 GLU cc_start: 0.5155 (mm-30) cc_final: 0.4906 (mm-30) REVERT: I 46 GLU cc_start: 0.8226 (tp30) cc_final: 0.7699 (tp30) REVERT: I 52 TYR cc_start: 0.7645 (m-80) cc_final: 0.7412 (m-80) REVERT: K 100 MET cc_start: 0.8694 (ppp) cc_final: 0.8412 (ppp) REVERT: K 122 LEU cc_start: 0.9448 (mt) cc_final: 0.9186 (mm) REVERT: M 100 MET cc_start: 0.8796 (mpp) cc_final: 0.8218 (mmp) REVERT: M 100 ASP cc_start: 0.8796 (p0) cc_final: 0.8570 (p0) REVERT: O 70 PHE cc_start: 0.7861 (m-10) cc_final: 0.7653 (m-10) REVERT: Q 530 MET cc_start: 0.8783 (mtm) cc_final: 0.8259 (mtm) REVERT: Q 595 ILE cc_start: 0.9233 (pt) cc_final: 0.8865 (mm) REVERT: Q 619 LEU cc_start: 0.9328 (pp) cc_final: 0.8950 (tt) REVERT: Q 638 TYR cc_start: 0.8172 (m-80) cc_final: 0.7520 (m-10) REVERT: R 12 MET cc_start: 0.6033 (mtp) cc_final: 0.5649 (mtp) REVERT: R 46 GLU cc_start: 0.8522 (tp30) cc_final: 0.8117 (tp30) REVERT: R 52 TYR cc_start: 0.7028 (m-10) cc_final: 0.6661 (m-10) REVERT: S 4 MET cc_start: 0.7645 (tpt) cc_final: 0.7241 (tpt) REVERT: S 5 THR cc_start: 0.7112 (m) cc_final: 0.6648 (m) REVERT: S 6 GLN cc_start: 0.6741 (mt0) cc_final: 0.6306 (mt0) REVERT: S 18 ARG cc_start: 0.7186 (ttt-90) cc_final: 0.6589 (mtp85) REVERT: S 24 ARG cc_start: 0.8273 (tmm160) cc_final: 0.8016 (tmm160) REVERT: S 48 MET cc_start: 0.5725 (ptm) cc_final: 0.5525 (ptm) outliers start: 1 outliers final: 0 residues processed: 501 average time/residue: 0.2095 time to fit residues: 170.3142 Evaluate side-chains 376 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 49 optimal weight: 8.9990 chunk 206 optimal weight: 40.0000 chunk 26 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 360 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 chunk 318 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 230 optimal weight: 0.2980 chunk 226 optimal weight: 9.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 67 ASN 2 103 GLN ** 2 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 478 ASN 6 52 ASN B 66 HIS B 203 GLN D 52 ASN J 6 GLN K 67 ASN K 315 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.101127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076047 restraints weight = 96302.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076119 restraints weight = 74394.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.076595 restraints weight = 60745.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.076905 restraints weight = 56720.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.077167 restraints weight = 52187.534| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 33405 Z= 0.258 Angle : 0.901 15.350 45741 Z= 0.423 Chirality : 0.050 0.471 5547 Planarity : 0.006 0.088 5469 Dihedral : 6.208 31.784 4152 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.15 % Allowed : 2.64 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 are not related in a simple way. whole: -1.96 (0.13), residues: 3768 helix: -0.13 (0.27), residues: 378 sheet: -0.57 (0.15), residues: 1137 loop : -1.98 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 61 TYR 0.027 0.002 TYR B 484 PHE 0.017 0.002 PHE B 382 TRP 0.047 0.002 TRP F 100F HIS 0.014 0.002 HIS P 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.26 (33168) covalent geometry : angle 0.85428 / 0.41 (45081) SS BOND : bond 0.00553 / 0.34 ( 51) SS BOND : angle 2.57401 / 1.60 ( 102) hydrogen bonds : bond 0.04390 / 2.91 ( 976) hydrogen bonds : angle 5.57210 / 3.80 ( 2652) link_ALPHA1-2 : bond 0.00279 / 0.17 ( 9) link_ALPHA1-2 : angle 1.77328 / 1.08 ( 27) link_ALPHA1-3 : bond 0.00785 / 0.51 ( 24) link_ALPHA1-3 : angle 2.04418 / 1.40 ( 72) link_ALPHA1-6 : bond 0.00577 / 0.34 ( 18) link_ALPHA1-6 : angle 1.74412 / 1.09 ( 54) link_BETA1-4 : bond 0.00600 / 0.37 ( 78) link_BETA1-4 : angle 2.38912 / 1.56 ( 234) link_NAG-ASN : bond 0.00701 / 0.43 ( 57) link_NAG-ASN : angle 3.16099 / 2.15 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 451 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 67 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7536 (p0) REVERT: 2 271 MET cc_start: 0.7534 (mtm) cc_final: 0.7304 (mtm) REVERT: 2 377 ASN cc_start: 0.8606 (t0) cc_final: 0.8299 (t0) REVERT: 2 504 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7496 (ttp-110) REVERT: 5 100 MET cc_start: 0.8915 (mpp) cc_final: 0.8559 (mpp) REVERT: 5 100 ASP cc_start: 0.8739 (p0) cc_final: 0.8521 (p0) REVERT: 7 79 ARG cc_start: 0.7536 (mpt180) cc_final: 0.7034 (mpt180) REVERT: 7 89 GLN cc_start: 0.7545 (pm20) cc_final: 0.6956 (pm20) REVERT: 8 51 ILE cc_start: 0.9232 (tt) cc_final: 0.8893 (mp) REVERT: 8 82 LEU cc_start: 0.9259 (mt) cc_final: 0.8915 (mt) REVERT: A 530 MET cc_start: 0.8059 (mtm) cc_final: 0.7145 (mtm) REVERT: A 591 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8965 (tm-30) REVERT: A 619 LEU cc_start: 0.9313 (pp) cc_final: 0.8945 (tt) REVERT: A 658 GLN cc_start: 0.8591 (tt0) cc_final: 0.7283 (tp40) REVERT: C 44 GLN cc_start: 0.8613 (pm20) cc_final: 0.8241 (pm20) REVERT: C 100 ASP cc_start: 0.8791 (p0) cc_final: 0.8530 (p0) REVERT: E 70 PHE cc_start: 0.8165 (m-80) cc_final: 0.7874 (m-10) REVERT: E 89 GLN cc_start: 0.7877 (pm20) cc_final: 0.7568 (pm20) REVERT: F 59 TYR cc_start: 0.7859 (m-80) cc_final: 0.7182 (m-80) REVERT: G 530 MET cc_start: 0.8424 (mtm) cc_final: 0.7502 (mtm) REVERT: G 591 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8744 (tm-30) REVERT: G 638 TYR cc_start: 0.8109 (m-80) cc_final: 0.7475 (m-10) REVERT: H 12 MET cc_start: 0.7188 (mtp) cc_final: 0.6662 (ttt) REVERT: H 46 GLU cc_start: 0.8402 (tp30) cc_final: 0.7771 (tp30) REVERT: H 77 HIS cc_start: 0.6813 (m90) cc_final: 0.6548 (m90) REVERT: I 16 GLU cc_start: 0.5117 (mm-30) cc_final: 0.4769 (mm-30) REVERT: I 46 GLU cc_start: 0.8260 (tp30) cc_final: 0.7737 (tp30) REVERT: J 88 CYS cc_start: 0.4524 (p) cc_final: 0.4177 (p) REVERT: K 122 LEU cc_start: 0.9484 (mt) cc_final: 0.9228 (mm) REVERT: M 44 GLN cc_start: 0.8778 (pm20) cc_final: 0.8568 (pm20) REVERT: M 100 MET cc_start: 0.8725 (mpp) cc_final: 0.8195 (mmp) REVERT: M 100 ASP cc_start: 0.8773 (p0) cc_final: 0.8553 (p0) REVERT: O 70 PHE cc_start: 0.7954 (m-10) cc_final: 0.7717 (m-10) REVERT: Q 530 MET cc_start: 0.8725 (mtm) cc_final: 0.8173 (mtm) REVERT: Q 595 ILE cc_start: 0.9288 (pt) cc_final: 0.8865 (mm) REVERT: Q 619 LEU cc_start: 0.9344 (pp) cc_final: 0.8920 (tt) REVERT: Q 638 TYR cc_start: 0.8036 (m-80) cc_final: 0.7455 (m-10) REVERT: R 12 MET cc_start: 0.6259 (mtp) cc_final: 0.5951 (mtp) REVERT: R 46 GLU cc_start: 0.8502 (tp30) cc_final: 0.8048 (tp30) REVERT: S 5 THR cc_start: 0.7210 (m) cc_final: 0.6881 (m) REVERT: S 18 ARG cc_start: 0.7216 (ttt-90) cc_final: 0.6578 (mtp85) REVERT: S 24 ARG cc_start: 0.8344 (tmm160) cc_final: 0.8022 (tmm160) outliers start: 5 outliers final: 0 residues processed: 456 average time/residue: 0.2123 time to fit residues: 156.2680 Evaluate side-chains 365 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 332 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 307 optimal weight: 7.9990 chunk 321 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 258 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 478 ASN 6 51 ASN 6 52 ASN 6 89 HIS ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN R 77 HIS S 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.080002 restraints weight = 94763.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080415 restraints weight = 68228.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081086 restraints weight = 56307.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.081375 restraints weight = 51052.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.081467 restraints weight = 47417.577| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 33405 Z= 0.133 Angle : 0.805 14.121 45741 Z= 0.378 Chirality : 0.047 0.459 5547 Planarity : 0.005 0.085 5469 Dihedral : 5.858 31.265 4152 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.06 % Allowed : 1.14 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.73 (0.14), residues: 3768 helix: 0.05 (0.28), residues: 378 sheet: -0.45 (0.15), residues: 1107 loop : -1.79 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG 7 53 TYR 0.026 0.001 TYR I 32 PHE 0.018 0.002 PHE H 78 TRP 0.051 0.002 TRP F 100F HIS 0.006 0.001 HIS L 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (33168) covalent geometry : angle 0.76514 / 0.37 (45081) SS BOND : bond 0.00363 / 0.23 ( 51) SS BOND : angle 2.22151 / 1.44 ( 102) hydrogen bonds : bond 0.03669 / 2.45 ( 976) hydrogen bonds : angle 5.39828 / 3.69 ( 2652) link_ALPHA1-2 : bond 0.00352 / 0.22 ( 9) link_ALPHA1-2 : angle 1.62877 / 1.03 ( 27) link_ALPHA1-3 : bond 0.00767 / 0.49 ( 24) link_ALPHA1-3 : angle 1.65861 / 1.16 ( 72) link_ALPHA1-6 : bond 0.00508 / 0.30 ( 18) link_ALPHA1-6 : angle 1.50914 / 0.99 ( 54) link_BETA1-4 : bond 0.00595 / 0.37 ( 78) link_BETA1-4 : angle 2.18859 / 1.45 ( 234) link_NAG-ASN : bond 0.00380 / 0.26 ( 57) link_NAG-ASN : angle 2.65794 / 1.83 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 516 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 195 ASN cc_start: 0.9013 (p0) cc_final: 0.8632 (p0) REVERT: 2 251 ILE cc_start: 0.9096 (tp) cc_final: 0.8730 (pt) REVERT: 2 271 MET cc_start: 0.7407 (mtm) cc_final: 0.7180 (mtm) REVERT: 2 377 ASN cc_start: 0.8548 (t0) cc_final: 0.8295 (t0) REVERT: 2 504 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7449 (ttp-110) REVERT: 5 100 MET cc_start: 0.8853 (mpp) cc_final: 0.8450 (mpp) REVERT: 5 100 ASP cc_start: 0.8752 (p0) cc_final: 0.8508 (p0) REVERT: 7 52 ARG cc_start: 0.8215 (tpm170) cc_final: 0.7900 (tpp-160) REVERT: 7 89 GLN cc_start: 0.7271 (pm20) cc_final: 0.6774 (pm20) REVERT: 8 51 ILE cc_start: 0.9043 (tt) cc_final: 0.8705 (mp) REVERT: A 530 MET cc_start: 0.8059 (mtm) cc_final: 0.7345 (mtm) REVERT: A 591 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8785 (tm-30) REVERT: A 595 ILE cc_start: 0.9228 (pt) cc_final: 0.8707 (mm) REVERT: A 619 LEU cc_start: 0.9251 (pp) cc_final: 0.8929 (tt) REVERT: A 658 GLN cc_start: 0.8497 (tt0) cc_final: 0.7165 (tp40) REVERT: B 161 MET cc_start: 0.8932 (tpp) cc_final: 0.8690 (tpp) REVERT: C 44 GLN cc_start: 0.8513 (pm20) cc_final: 0.8145 (pm20) REVERT: C 100 MET cc_start: 0.8769 (mpp) cc_final: 0.8249 (mpp) REVERT: C 100 ASP cc_start: 0.8760 (p0) cc_final: 0.8499 (p0) REVERT: E 70 PHE cc_start: 0.8054 (m-80) cc_final: 0.7793 (m-10) REVERT: E 89 GLN cc_start: 0.7602 (pm20) cc_final: 0.7291 (pm20) REVERT: F 59 TYR cc_start: 0.7371 (m-80) cc_final: 0.6771 (m-80) REVERT: G 530 MET cc_start: 0.8354 (mtm) cc_final: 0.7722 (mtm) REVERT: G 591 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8750 (tm-30) REVERT: G 638 TYR cc_start: 0.8080 (m-80) cc_final: 0.7634 (m-10) REVERT: G 658 GLN cc_start: 0.8601 (tt0) cc_final: 0.6913 (tp40) REVERT: H 12 MET cc_start: 0.7122 (mtp) cc_final: 0.6609 (ttt) REVERT: H 46 GLU cc_start: 0.8424 (tp30) cc_final: 0.7797 (tp30) REVERT: H 77 HIS cc_start: 0.6877 (m90) cc_final: 0.6520 (m90) REVERT: I 32 TYR cc_start: 0.8639 (m-80) cc_final: 0.8309 (m-80) REVERT: I 46 GLU cc_start: 0.8191 (tp30) cc_final: 0.7699 (tp30) REVERT: K 100 MET cc_start: 0.8749 (ppp) cc_final: 0.8384 (ppp) REVERT: K 122 LEU cc_start: 0.9396 (mt) cc_final: 0.9175 (mm) REVERT: K 161 MET cc_start: 0.8868 (tpp) cc_final: 0.8593 (tpp) REVERT: K 195 ASN cc_start: 0.8882 (p0) cc_final: 0.8533 (p0) REVERT: K 377 ASN cc_start: 0.8590 (t0) cc_final: 0.8389 (t0) REVERT: L 6 GLN cc_start: 0.7014 (mt0) cc_final: 0.6806 (mt0) REVERT: L 48 MET cc_start: 0.6762 (ptm) cc_final: 0.6478 (ptm) REVERT: M 47 TRP cc_start: 0.8446 (t60) cc_final: 0.8046 (t60) REVERT: M 100 MET cc_start: 0.8704 (mpp) cc_final: 0.7889 (mmt) REVERT: M 100 ASP cc_start: 0.8726 (p0) cc_final: 0.8499 (p0) REVERT: O 70 PHE cc_start: 0.7724 (m-10) cc_final: 0.7496 (m-10) REVERT: P 84 PRO cc_start: 0.8643 (Cg_exo) cc_final: 0.8354 (Cg_endo) REVERT: P 101 GLN cc_start: 0.8414 (tt0) cc_final: 0.7760 (tp-100) REVERT: Q 530 MET cc_start: 0.8589 (mtm) cc_final: 0.7987 (mtm) REVERT: Q 591 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8802 (tm-30) REVERT: Q 595 ILE cc_start: 0.9194 (pt) cc_final: 0.8847 (mm) REVERT: Q 619 LEU cc_start: 0.9285 (pp) cc_final: 0.8908 (tt) REVERT: Q 638 TYR cc_start: 0.8098 (m-80) cc_final: 0.7519 (m-10) REVERT: Q 658 GLN cc_start: 0.8441 (tt0) cc_final: 0.7011 (tp40) REVERT: R 32 TYR cc_start: 0.8443 (m-10) cc_final: 0.8166 (m-80) REVERT: R 46 GLU cc_start: 0.8516 (tp30) cc_final: 0.8084 (tp30) REVERT: S 4 MET cc_start: 0.7561 (tpt) cc_final: 0.7222 (tpt) REVERT: S 5 THR cc_start: 0.6986 (m) cc_final: 0.6504 (m) REVERT: S 24 ARG cc_start: 0.8316 (tmm160) cc_final: 0.8001 (tmm160) outliers start: 2 outliers final: 1 residues processed: 517 average time/residue: 0.2112 time to fit residues: 176.8291 Evaluate side-chains 393 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 266 optimal weight: 8.9990 chunk 348 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 330 optimal weight: 7.9990 chunk 265 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 478 ASN B 66 HIS D 52 ASN J 6 GLN ** K 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 HIS R 77 HIS S 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.103289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078579 restraints weight = 95437.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.078816 restraints weight = 68150.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.079182 restraints weight = 55723.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.079639 restraints weight = 55386.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079699 restraints weight = 48034.234| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33405 Z= 0.185 Angle : 0.834 15.251 45741 Z= 0.392 Chirality : 0.048 0.387 5547 Planarity : 0.005 0.084 5469 Dihedral : 5.879 32.828 4152 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.09 % Allowed : 0.72 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.61 (0.14), residues: 3768 helix: 0.42 (0.29), residues: 360 sheet: -0.33 (0.16), residues: 1062 loop : -1.76 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 79 TYR 0.025 0.002 TYR B 484 PHE 0.018 0.002 PHE S 62 TRP 0.066 0.002 TRP P 36 HIS 0.009 0.001 HIS P 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (33168) covalent geometry : angle 0.79316 / 0.38 (45081) SS BOND : bond 0.00426 / 0.27 ( 51) SS BOND : angle 2.35534 / 1.50 ( 102) hydrogen bonds : bond 0.03910 / 2.60 ( 976) hydrogen bonds : angle 5.38690 / 3.67 ( 2652) link_ALPHA1-2 : bond 0.00266 / 0.16 ( 9) link_ALPHA1-2 : angle 1.68845 / 1.05 ( 27) link_ALPHA1-3 : bond 0.00705 / 0.44 ( 24) link_ALPHA1-3 : angle 1.84192 / 1.28 ( 72) link_ALPHA1-6 : bond 0.00527 / 0.32 ( 18) link_ALPHA1-6 : angle 1.60733 / 1.02 ( 54) link_BETA1-4 : bond 0.00571 / 0.35 ( 78) link_BETA1-4 : angle 2.21260 / 1.45 ( 234) link_NAG-ASN : bond 0.00484 / 0.32 ( 57) link_NAG-ASN : angle 2.76075 / 1.88 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 475 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 104 MET cc_start: 0.8223 (ttp) cc_final: 0.8013 (ttp) REVERT: 2 195 ASN cc_start: 0.9076 (p0) cc_final: 0.8728 (p0) REVERT: 2 251 ILE cc_start: 0.9153 (tp) cc_final: 0.8842 (pt) REVERT: 2 271 MET cc_start: 0.7513 (mtm) cc_final: 0.7296 (mtm) REVERT: 2 377 ASN cc_start: 0.8570 (t0) cc_final: 0.8292 (t0) REVERT: 2 504 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7519 (ttp-110) REVERT: 5 100 TYR cc_start: 0.8770 (p90) cc_final: 0.8345 (p90) REVERT: 5 100 MET cc_start: 0.8856 (mpp) cc_final: 0.8483 (mpp) REVERT: 5 100 ASP cc_start: 0.8766 (p0) cc_final: 0.8547 (p0) REVERT: 7 51 SER cc_start: 0.8867 (p) cc_final: 0.8223 (p) REVERT: 7 89 GLN cc_start: 0.7381 (pm20) cc_final: 0.6971 (pm20) REVERT: 8 51 ILE cc_start: 0.9116 (tt) cc_final: 0.8813 (mp) REVERT: A 530 MET cc_start: 0.8088 (mtm) cc_final: 0.7419 (mtm) REVERT: A 591 GLN cc_start: 0.9320 (tm-30) cc_final: 0.8854 (tm-30) REVERT: A 595 ILE cc_start: 0.9212 (pt) cc_final: 0.8611 (mm) REVERT: A 619 LEU cc_start: 0.9256 (pp) cc_final: 0.8929 (tt) REVERT: A 658 GLN cc_start: 0.8443 (tt0) cc_final: 0.7151 (tp40) REVERT: B 161 MET cc_start: 0.8948 (tpp) cc_final: 0.8667 (tpp) REVERT: C 44 GLN cc_start: 0.8553 (pm20) cc_final: 0.8205 (pm20) REVERT: C 100 MET cc_start: 0.8743 (mpp) cc_final: 0.8314 (mpp) REVERT: C 100 ASP cc_start: 0.8797 (p0) cc_final: 0.8554 (p0) REVERT: E 34 TRP cc_start: 0.7515 (m100) cc_final: 0.7061 (m-10) REVERT: E 89 GLN cc_start: 0.7715 (pm20) cc_final: 0.7365 (pm20) REVERT: F 59 TYR cc_start: 0.7600 (m-80) cc_final: 0.6837 (m-80) REVERT: F 80 MET cc_start: 0.7536 (ttp) cc_final: 0.7256 (ptm) REVERT: G 530 MET cc_start: 0.8583 (mtm) cc_final: 0.7461 (mtm) REVERT: G 591 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8737 (tm-30) REVERT: G 638 TYR cc_start: 0.8158 (m-80) cc_final: 0.7586 (m-10) REVERT: G 658 GLN cc_start: 0.8578 (tt0) cc_final: 0.6897 (tp40) REVERT: H 12 MET cc_start: 0.7132 (mtp) cc_final: 0.6628 (ttt) REVERT: H 46 GLU cc_start: 0.8436 (tp30) cc_final: 0.7796 (tp30) REVERT: H 77 HIS cc_start: 0.6791 (m90) cc_final: 0.6493 (m90) REVERT: I 46 GLU cc_start: 0.8341 (tp30) cc_final: 0.7762 (tp30) REVERT: J 88 CYS cc_start: 0.5469 (p) cc_final: 0.4705 (p) REVERT: K 100 MET cc_start: 0.8788 (ppp) cc_final: 0.8468 (ppp) REVERT: K 122 LEU cc_start: 0.9440 (mt) cc_final: 0.9182 (mm) REVERT: K 195 ASN cc_start: 0.8936 (p0) cc_final: 0.8596 (p0) REVERT: M 100 ASP cc_start: 0.8745 (p0) cc_final: 0.8537 (p0) REVERT: O 70 PHE cc_start: 0.7848 (m-10) cc_final: 0.7556 (m-10) REVERT: P 84 PRO cc_start: 0.8650 (Cg_exo) cc_final: 0.8392 (Cg_endo) REVERT: Q 530 MET cc_start: 0.8634 (mtm) cc_final: 0.8040 (mtm) REVERT: Q 591 GLN cc_start: 0.9252 (tm-30) cc_final: 0.8903 (tm-30) REVERT: Q 595 ILE cc_start: 0.9242 (pt) cc_final: 0.8879 (mm) REVERT: Q 619 LEU cc_start: 0.9309 (pp) cc_final: 0.8890 (tt) REVERT: Q 638 TYR cc_start: 0.8051 (m-80) cc_final: 0.7448 (m-10) REVERT: Q 658 GLN cc_start: 0.8418 (tt0) cc_final: 0.6998 (tp40) REVERT: R 32 TYR cc_start: 0.8428 (m-10) cc_final: 0.7918 (m-80) REVERT: R 46 GLU cc_start: 0.8515 (tp30) cc_final: 0.8026 (tp30) REVERT: R 100 LEU cc_start: 0.6245 (pp) cc_final: 0.5874 (tt) REVERT: S 5 THR cc_start: 0.6983 (m) cc_final: 0.6652 (m) REVERT: S 24 ARG cc_start: 0.8330 (tmm160) cc_final: 0.7973 (tmm160) outliers start: 3 outliers final: 0 residues processed: 477 average time/residue: 0.2118 time to fit residues: 163.8597 Evaluate side-chains 378 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 77 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 314 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 311 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 359 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 232 optimal weight: 40.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 52 ASN A 575 GLN B 66 HIS D 52 ASN J 6 GLN ** K 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.103884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.079253 restraints weight = 95755.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.079430 restraints weight = 70956.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.079981 restraints weight = 55554.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.080407 restraints weight = 51726.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.080463 restraints weight = 48109.787| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33405 Z= 0.164 Angle : 0.815 15.068 45741 Z= 0.385 Chirality : 0.048 0.351 5547 Planarity : 0.005 0.084 5469 Dihedral : 5.823 31.878 4152 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.09 % Allowed : 0.42 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.62 (0.14), residues: 3768 helix: 0.44 (0.29), residues: 363 sheet: -0.41 (0.16), residues: 1110 loop : -1.75 (0.13), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 5 38 TYR 0.021 0.001 TYR B 484 PHE 0.019 0.002 PHE R 78 TRP 0.060 0.002 TRP P 36 HIS 0.007 0.001 HIS 8 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (33168) covalent geometry : angle 0.77548 / 0.38 (45081) SS BOND : bond 0.00405 / 0.26 ( 51) SS BOND : angle 2.35569 / 1.48 ( 102) hydrogen bonds : bond 0.03818 / 2.55 ( 976) hydrogen bonds : angle 5.34187 / 3.64 ( 2652) link_ALPHA1-2 : bond 0.00291 / 0.18 ( 9) link_ALPHA1-2 : angle 1.64012 / 1.03 ( 27) link_ALPHA1-3 : bond 0.00716 / 0.45 ( 24) link_ALPHA1-3 : angle 1.74336 / 1.21 ( 72) link_ALPHA1-6 : bond 0.00491 / 0.29 ( 18) link_ALPHA1-6 : angle 1.56175 / 1.00 ( 54) link_BETA1-4 : bond 0.00569 / 0.35 ( 78) link_BETA1-4 : angle 2.16631 / 1.42 ( 234) link_NAG-ASN : bond 0.00454 / 0.28 ( 57) link_NAG-ASN : angle 2.64671 / 1.80 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 469 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 104 MET cc_start: 0.8219 (ttp) cc_final: 0.7954 (ttp) REVERT: 2 195 ASN cc_start: 0.9058 (p0) cc_final: 0.8672 (p0) REVERT: 2 251 ILE cc_start: 0.9149 (tp) cc_final: 0.8872 (pt) REVERT: 2 271 MET cc_start: 0.7499 (mtm) cc_final: 0.7285 (mtm) REVERT: 2 377 ASN cc_start: 0.8585 (t0) cc_final: 0.8310 (t0) REVERT: 2 504 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7462 (ttp-110) REVERT: 5 100 MET cc_start: 0.8846 (mpp) cc_final: 0.8456 (mpp) REVERT: 5 100 ASP cc_start: 0.8757 (p0) cc_final: 0.8529 (p0) REVERT: 7 89 GLN cc_start: 0.7343 (pm20) cc_final: 0.6971 (pm20) REVERT: 8 51 ILE cc_start: 0.9102 (tt) cc_final: 0.8813 (mp) REVERT: 8 82 PHE cc_start: 0.7443 (t80) cc_final: 0.7241 (t80) REVERT: A 530 MET cc_start: 0.8010 (mtm) cc_final: 0.7346 (mtm) REVERT: A 591 GLN cc_start: 0.9289 (tm-30) cc_final: 0.8798 (tm-30) REVERT: A 595 ILE cc_start: 0.9180 (pt) cc_final: 0.8609 (mm) REVERT: A 619 LEU cc_start: 0.9265 (pp) cc_final: 0.8895 (tt) REVERT: A 658 GLN cc_start: 0.8383 (tt0) cc_final: 0.7106 (tp40) REVERT: B 161 MET cc_start: 0.8950 (tpp) cc_final: 0.8674 (tpp) REVERT: C 44 GLN cc_start: 0.8535 (pm20) cc_final: 0.8200 (pm20) REVERT: C 100 ASP cc_start: 0.8803 (p0) cc_final: 0.8548 (p0) REVERT: E 34 TRP cc_start: 0.7363 (m100) cc_final: 0.7031 (m-10) REVERT: E 89 GLN cc_start: 0.7616 (pm20) cc_final: 0.7032 (pm20) REVERT: F 59 TYR cc_start: 0.7577 (m-80) cc_final: 0.7208 (m-80) REVERT: F 82 LEU cc_start: 0.9322 (mt) cc_final: 0.9069 (mt) REVERT: G 530 MET cc_start: 0.8408 (mtm) cc_final: 0.7325 (mtm) REVERT: G 591 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8703 (tm-30) REVERT: G 638 TYR cc_start: 0.8134 (m-80) cc_final: 0.7528 (m-10) REVERT: G 658 GLN cc_start: 0.8511 (tt0) cc_final: 0.6906 (tp40) REVERT: H 12 MET cc_start: 0.7122 (mtp) cc_final: 0.6617 (ttt) REVERT: H 46 GLU cc_start: 0.8451 (tp30) cc_final: 0.7840 (tp30) REVERT: H 77 HIS cc_start: 0.6760 (m90) cc_final: 0.6494 (m90) REVERT: I 46 GLU cc_start: 0.8228 (tp30) cc_final: 0.7683 (tp30) REVERT: J 48 MET cc_start: 0.6681 (ptm) cc_final: 0.6408 (ptm) REVERT: J 88 CYS cc_start: 0.5449 (p) cc_final: 0.4669 (p) REVERT: K 100 MET cc_start: 0.8814 (ppp) cc_final: 0.8461 (ppp) REVERT: K 122 LEU cc_start: 0.9410 (mt) cc_final: 0.9157 (mm) REVERT: K 195 ASN cc_start: 0.8849 (p0) cc_final: 0.8515 (p0) REVERT: M 100 MET cc_start: 0.8732 (mpp) cc_final: 0.8516 (mpp) REVERT: M 100 ASP cc_start: 0.8734 (p0) cc_final: 0.8516 (p0) REVERT: O 66 SER cc_start: 0.7942 (t) cc_final: 0.7290 (p) REVERT: O 70 PHE cc_start: 0.7701 (m-10) cc_final: 0.7469 (m-10) REVERT: O 81 ASP cc_start: 0.7746 (m-30) cc_final: 0.7482 (m-30) REVERT: P 84 PRO cc_start: 0.8614 (Cg_exo) cc_final: 0.8343 (Cg_endo) REVERT: Q 530 MET cc_start: 0.8601 (mtm) cc_final: 0.8164 (mtt) REVERT: Q 595 ILE cc_start: 0.9190 (pt) cc_final: 0.8899 (mm) REVERT: Q 619 LEU cc_start: 0.9303 (pp) cc_final: 0.9013 (tt) REVERT: Q 622 ILE cc_start: 0.8005 (pt) cc_final: 0.7685 (mp) REVERT: Q 638 TYR cc_start: 0.8090 (m-80) cc_final: 0.7528 (m-10) REVERT: R 46 GLU cc_start: 0.8530 (tp30) cc_final: 0.8090 (tp30) REVERT: S 5 THR cc_start: 0.6943 (m) cc_final: 0.6634 (m) REVERT: S 24 ARG cc_start: 0.8339 (tmm160) cc_final: 0.7981 (tmm160) REVERT: S 48 MET cc_start: 0.6295 (ptm) cc_final: 0.5862 (ptm) outliers start: 3 outliers final: 1 residues processed: 472 average time/residue: 0.2096 time to fit residues: 160.7653 Evaluate side-chains 376 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 108 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 369 optimal weight: 9.9990 chunk 368 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 94 ASN B 66 HIS D 52 ASN J 6 GLN ** K 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 HIS S 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.079653 restraints weight = 95499.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.079847 restraints weight = 67917.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080205 restraints weight = 54962.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.080608 restraints weight = 55843.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080707 restraints weight = 48341.304| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33405 Z= 0.156 Angle : 0.803 14.999 45741 Z= 0.380 Chirality : 0.047 0.332 5547 Planarity : 0.005 0.084 5469 Dihedral : 5.800 32.059 4152 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.54 (0.14), residues: 3768 helix: 0.61 (0.29), residues: 360 sheet: -0.39 (0.15), residues: 1122 loop : -1.69 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG 5 38 TYR 0.023 0.002 TYR C 100B PHE 0.028 0.002 PHE R 78 TRP 0.055 0.002 TRP P 36 HIS 0.010 0.001 HIS P 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (33168) covalent geometry : angle 0.76392 / 0.37 (45081) SS BOND : bond 0.00433 / 0.29 ( 51) SS BOND : angle 2.27054 / 1.48 ( 102) hydrogen bonds : bond 0.03727 / 2.48 ( 976) hydrogen bonds : angle 5.32142 / 3.62 ( 2652) link_ALPHA1-2 : bond 0.00290 / 0.18 ( 9) link_ALPHA1-2 : angle 1.63222 / 1.02 ( 27) link_ALPHA1-3 : bond 0.00707 / 0.44 ( 24) link_ALPHA1-3 : angle 1.73625 / 1.21 ( 72) link_ALPHA1-6 : bond 0.00491 / 0.29 ( 18) link_ALPHA1-6 : angle 1.55887 / 1.00 ( 54) link_BETA1-4 : bond 0.00557 / 0.35 ( 78) link_BETA1-4 : angle 2.13679 / 1.40 ( 234) link_NAG-ASN : bond 0.00448 / 0.30 ( 57) link_NAG-ASN : angle 2.59583 / 1.77 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5031.31 seconds wall clock time: 88 minutes 53.45 seconds (5333.45 seconds total)