Starting phenix.real_space_refine on Mon Sep 14 19:35:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jx7_9891/09_2026/6jx7_9891.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jx7_9891/09_2026/6jx7_9891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jx7_9891/09_2026/6jx7_9891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jx7_9891/09_2026/6jx7_9891.map" model { file = "/net/cci-nas-00/data/ceres_data/6jx7_9891/09_2026/6jx7_9891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jx7_9891/09_2026/6jx7_9891.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6jx7_9891/09_2026/6jx7_9891.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jx7_9891/09_2026/6jx7_9891.cif" } resolution = 3.31 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= -0.008 sd= 0.895 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 156 5.16 5 C 20265 2.51 5 N 4938 2.21 5 O 6756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.16s 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: 32115 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "B" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "C" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "D" 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: "E" 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: "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: 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: "H" 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: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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: 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: "N" 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: "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: 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: "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 Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "S" 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: "T" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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: 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: 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: "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: 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: "Z" 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: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "b" 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: "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: 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: "e" 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: "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: 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: "h" 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: "i" 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: "j" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: 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: "l" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "m" 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: "n" 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: "o" 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: "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: 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: "r" 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: "s" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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: 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: 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: "3" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "4" 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: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.56, per 1000 atoms: 0.24 Number of scatterers: 32115 At special positions: 0 Unit cell: (180.96, 194.01, 180.09, 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 156 16.00 O 6756 8.00 N 4938 7.00 C 20265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 178 " distance=2.05 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 510 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 644 " distance=2.05 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 702 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 820 " - pdb=" SG CYS A 832 " distance=2.03 Simple disulfide: pdb=" SG CYS A 889 " - pdb=" SG CYS A 911 " distance=2.03 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS A1003 " - pdb=" SG CYS A1014 " distance=2.03 Simple disulfide: pdb=" SG CYS A1205 " - pdb=" SG CYS A1216 " distance=2.02 Simple disulfide: pdb=" SG CYS A1255 " - pdb=" SG CYS A1302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 178 " distance=2.05 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 510 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 644 " distance=2.05 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 702 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 820 " - pdb=" SG CYS B 832 " distance=2.03 Simple disulfide: pdb=" SG CYS B 889 " - pdb=" SG CYS B 911 " distance=2.03 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B1003 " - pdb=" SG CYS B1014 " distance=2.03 Simple disulfide: pdb=" SG CYS B1205 " - pdb=" SG CYS B1216 " distance=2.02 Simple disulfide: pdb=" SG CYS B1255 " - pdb=" SG CYS B1302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 178 " distance=2.05 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 510 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 644 " distance=2.05 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 702 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 820 " - pdb=" SG CYS C 832 " distance=2.03 Simple disulfide: pdb=" SG CYS C 889 " - pdb=" SG CYS C 911 " distance=2.03 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS C1003 " - pdb=" SG CYS C1014 " distance=2.03 Simple disulfide: pdb=" SG CYS C1205 " - pdb=" SG CYS C1216 " distance=2.02 Simple disulfide: pdb=" SG CYS C1255 " - pdb=" SG CYS C1302 " distance=2.03 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=3, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN I 4 " - " MAN I 5 " " MAN T 4 " - " MAN T 5 " " MAN a 4 " - " MAN a 5 " " MAN l 4 " - " MAN l 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 2 3 " - " MAN 2 4 " " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA I 3 " - " MAN I 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA a 3 " - " MAN a 4 " " BMA k 3 " - " MAN k 4 " " BMA l 3 " - " MAN l 4 " " MAN l 6 " - " MAN l 7 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA 2 3 " - " MAN 2 5 " " BMA 3 3 " - " MAN 3 6 " " BMA I 3 " - " MAN I 6 " " MAN I 6 " - " MAN I 7 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 5 " " BMA T 3 " - " MAN T 6 " " BMA a 3 " - " MAN a 6 " " MAN a 6 " - " MAN a 7 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA g 3 " - " MAN g 4 " " BMA h 3 " - " MAN h 4 " " BMA k 3 " - " MAN k 5 " " BMA l 3 " - " MAN l 6 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 7 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG D 1 " - " NAG D 2 " " 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 H 2 " - " BMA H 3 " " 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 N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 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 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 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " 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 f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " 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 r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 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 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 " BETA1-6 " NAG 1 1 " - " FUC 1 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 4 " " NAG j 1 " - " FUC j 4 " NAG-ASN " NAG 0 1 " - " ASN C 868 " " NAG 1 1 " - " ASN C 949 " " NAG 2 1 " - " ASN C1092 " " NAG 3 1 " - " ASN C1218 " " NAG 4 1 " - " ASN C1308 " " NAG A1508 " - " ASN A 260 " " NAG A1522 " - " ASN A 380 " " NAG A1523 " - " ASN A 464 " " NAG A1535 " - " ASN A 585 " " NAG A1536 " - " ASN A 590 " " NAG A1541 " - " ASN A 819 " " NAG A1568 " - " ASN A1257 " " NAG A1569 " - " ASN A1275 " " NAG A1572 " - " ASN A1325 " " NAG B1508 " - " ASN B 260 " " NAG B1522 " - " ASN B 380 " " NAG B1523 " - " ASN B 464 " " NAG B1535 " - " ASN B 585 " " NAG B1536 " - " ASN B 590 " " NAG B1541 " - " ASN B 819 " " NAG B1568 " - " ASN B1257 " " NAG B1569 " - " ASN B1275 " " NAG B1572 " - " ASN B1325 " " NAG C1509 " - " ASN C 260 " " NAG C1523 " - " ASN C 380 " " NAG C1524 " - " ASN C 464 " " NAG C1536 " - " ASN C 585 " " NAG C1537 " - " ASN C 590 " " NAG C1542 " - " ASN C 819 " " NAG C1569 " - " ASN C1257 " " NAG C1570 " - " ASN C1275 " " NAG C1573 " - " ASN C1325 " " NAG D 1 " - " ASN A 161 " " NAG E 1 " - " ASN A 246 " " NAG F 1 " - " ASN A 254 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 346 " " NAG I 1 " - " ASN A 357 " " NAG J 1 " - " ASN A 482 " " NAG K 1 " - " ASN A 491 " " NAG L 1 " - " ASN A 547 " " NAG M 1 " - " ASN A 774 " " NAG N 1 " - " ASN A 814 " " NAG O 1 " - " ASN A 841 " " NAG P 1 " - " ASN A 862 " " NAG Q 1 " - " ASN A 868 " " NAG R 1 " - " ASN A 949 " " NAG S 1 " - " ASN A1092 " " NAG T 1 " - " ASN A1218 " " NAG U 1 " - " ASN A1308 " " NAG V 1 " - " ASN B 161 " " NAG W 1 " - " ASN B 246 " " NAG X 1 " - " ASN B 254 " " NAG Y 1 " - " ASN B 331 " " NAG Z 1 " - " ASN B 346 " " NAG a 1 " - " ASN B 357 " " NAG b 1 " - " ASN B 482 " " NAG c 1 " - " ASN B 491 " " NAG d 1 " - " ASN B 547 " " NAG e 1 " - " ASN B 774 " " NAG f 1 " - " ASN B 814 " " NAG g 1 " - " ASN B 841 " " NAG h 1 " - " ASN B 862 " " NAG i 1 " - " ASN B 868 " " NAG j 1 " - " ASN B 949 " " NAG k 1 " - " ASN B1092 " " NAG l 1 " - " ASN B1218 " " NAG m 1 " - " ASN B1308 " " NAG n 1 " - " ASN C 161 " " NAG o 1 " - " ASN C 246 " " NAG p 1 " - " ASN C 254 " " NAG q 1 " - " ASN C 331 " " NAG r 1 " - " ASN C 346 " " NAG s 1 " - " ASN C 357 " " NAG t 1 " - " ASN C 482 " " NAG u 1 " - " ASN C 491 " " NAG v 1 " - " ASN C 547 " " NAG w 1 " - " ASN C 774 " " NAG x 1 " - " ASN C 814 " " NAG y 1 " - " ASN C 841 " " NAG z 1 " - " ASN C 862 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7032 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 54 sheets defined 22.6% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 513 removed outlier: 3.556A pdb=" N ILE A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 574' Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR A 892 " --> pdb=" O ASP A 888 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 893 " --> pdb=" O CYS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN A 902 " --> pdb=" O ARG A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 902' Processing helix chain 'A' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN A 906 " --> pdb=" O LEU A 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 903 through 906' Processing helix chain 'A' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 915 " --> pdb=" O CYS A 911 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 970 removed outlier: 4.194A pdb=" N SER A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 969 " --> pdb=" O GLY A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 985 Processing helix chain 'A' and resid 1011 through 1019 removed outlier: 3.784A pdb=" N ASN A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY A1043 " --> pdb=" O SER A1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A1045 " --> pdb=" O ILE A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 removed outlier: 3.873A pdb=" N ASN A1066 " --> pdb=" O GLN A1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A1080 " --> pdb=" O GLN A1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A1098 " --> pdb=" O THR A1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER A1116 " --> pdb=" O ASN A1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A1117 " --> pdb=" O SER A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU A1132 " --> pdb=" O GLN A1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A1133 " --> pdb=" O GLY A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1140 No H-bonds generated for 'chain 'A' and resid 1138 through 1140' Processing helix chain 'A' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA A1164 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A1168 " --> pdb=" O ALA A1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A1169 " --> pdb=" O GLN A1165 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A1187 " --> pdb=" O GLN A1183 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A1200 " --> pdb=" O GLN A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1294 No H-bonds generated for 'chain 'A' and resid 1292 through 1294' Processing helix chain 'A' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU A1316 " --> pdb=" O THR A1312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1317 " --> pdb=" O THR A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR A1327 " --> pdb=" O ASP A1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A1329 " --> pdb=" O ASN A1325 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A1330 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A1331 " --> pdb=" O THR A1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 removed outlier: 3.556A pdb=" N ILE B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU B 571 " --> pdb=" O GLY B 567 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 573 " --> pdb=" O PRO B 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 567 through 574' Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR B 892 " --> pdb=" O ASP B 888 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 893 " --> pdb=" O CYS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU B 901 " --> pdb=" O ASN B 897 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B 902 " --> pdb=" O ARG B 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 897 through 902' Processing helix chain 'B' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN B 906 " --> pdb=" O LEU B 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 903 through 906' Processing helix chain 'B' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR B 913 " --> pdb=" O SER B 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 914 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 915 " --> pdb=" O CYS B 911 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 925 " --> pdb=" O GLY B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU B 941 " --> pdb=" O ASP B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 970 removed outlier: 4.193A pdb=" N SER B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 969 " --> pdb=" O GLY B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 985 Processing helix chain 'B' and resid 1011 through 1019 removed outlier: 3.783A pdb=" N ASN B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY B1043 " --> pdb=" O SER B1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET B1044 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B1045 " --> pdb=" O ILE B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1067 removed outlier: 3.872A pdb=" N ASN B1066 " --> pdb=" O GLN B1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B1067 " --> pdb=" O ALA B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B1080 " --> pdb=" O GLN B1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B1098 " --> pdb=" O THR B1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B1099 " --> pdb=" O LEU B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER B1116 " --> pdb=" O ASN B1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B1117 " --> pdb=" O SER B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU B1132 " --> pdb=" O GLN B1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER B1133 " --> pdb=" O GLY B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1140 No H-bonds generated for 'chain 'B' and resid 1138 through 1140' Processing helix chain 'B' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE B1153 " --> pdb=" O SER B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA B1164 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B1168 " --> pdb=" O ALA B1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B1169 " --> pdb=" O GLN B1165 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B1183 " --> pdb=" O ALA B1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B1187 " --> pdb=" O GLN B1183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B1200 " --> pdb=" O GLN B1196 " (cutoff:3.500A) Processing helix chain 'B' and resid 1292 through 1294 No H-bonds generated for 'chain 'B' and resid 1292 through 1294' Processing helix chain 'B' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN B1315 " --> pdb=" O HIS B1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU B1316 " --> pdb=" O THR B1312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B1317 " --> pdb=" O THR B1313 " (cutoff:3.500A) Processing helix chain 'B' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR B1327 " --> pdb=" O ASP B1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B1329 " --> pdb=" O ASN B1325 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP B1330 " --> pdb=" O LYS B1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B1331 " --> pdb=" O THR B1327 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 513 removed outlier: 3.555A pdb=" N ILE C 508 " --> pdb=" O PRO C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 566 Processing helix chain 'C' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 573 " --> pdb=" O PRO C 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 567 through 574' Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR C 892 " --> pdb=" O ASP C 888 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 893 " --> pdb=" O CYS C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU C 901 " --> pdb=" O ASN C 897 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN C 902 " --> pdb=" O ARG C 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 897 through 902' Processing helix chain 'C' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN C 906 " --> pdb=" O LEU C 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 903 through 906' Processing helix chain 'C' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR C 913 " --> pdb=" O SER C 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 914 " --> pdb=" O ALA C 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 915 " --> pdb=" O CYS C 911 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY C 921 " --> pdb=" O SER C 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 970 removed outlier: 4.194A pdb=" N SER C 968 " --> pdb=" O ASP C 964 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 969 " --> pdb=" O GLY C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 985 Processing helix chain 'C' and resid 1011 through 1019 removed outlier: 3.783A pdb=" N ASN C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY C1043 " --> pdb=" O SER C1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C1045 " --> pdb=" O ILE C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1067 removed outlier: 3.873A pdb=" N ASN C1066 " --> pdb=" O GLN C1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C1067 " --> pdb=" O ALA C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN C1079 " --> pdb=" O LEU C1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C1080 " --> pdb=" O GLN C1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C1098 " --> pdb=" O THR C1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C1099 " --> pdb=" O LEU C1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER C1116 " --> pdb=" O ASN C1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C1117 " --> pdb=" O SER C1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU C1132 " --> pdb=" O GLN C1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER C1133 " --> pdb=" O GLY C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1140 No H-bonds generated for 'chain 'C' and resid 1138 through 1140' Processing helix chain 'C' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE C1153 " --> pdb=" O SER C1149 " (cutoff:3.500A) Processing helix chain 'C' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA C1164 " --> pdb=" O VAL C1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN C1165 " --> pdb=" O GLU C1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C1168 " --> pdb=" O ALA C1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C1169 " --> pdb=" O GLN C1165 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C1183 " --> pdb=" O ALA C1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C1187 " --> pdb=" O GLN C1183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C1200 " --> pdb=" O GLN C1196 " (cutoff:3.500A) Processing helix chain 'C' and resid 1292 through 1294 No H-bonds generated for 'chain 'C' and resid 1292 through 1294' Processing helix chain 'C' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN C1315 " --> pdb=" O HIS C1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C1316 " --> pdb=" O THR C1312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C1317 " --> pdb=" O THR C1313 " (cutoff:3.500A) Processing helix chain 'C' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR C1327 " --> pdb=" O ASP C1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C1329 " --> pdb=" O ASN C1325 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP C1330 " --> pdb=" O LYS C1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C1331 " --> pdb=" O THR C1327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA A 227 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A 107 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 124 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 151 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 180 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN A 199 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 324 removed outlier: 3.785A pdb=" N VAL A 312 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 482 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 320 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR A 480 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS A 322 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 478 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE A 447 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 324 removed outlier: 3.785A pdb=" N VAL A 312 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 482 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 320 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR A 480 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS A 322 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 478 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP A 485 " --> pdb=" O TYR A 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR A 500 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 487 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU A 498 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP A 489 " --> pdb=" O THR A 496 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA A 334 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 383 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387 removed outlier: 5.796A pdb=" N TYR A 413 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 431 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N CYS A 415 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 427 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE A 770 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 809 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 771 " --> pdb=" O TYR A 807 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 807 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.503A pdb=" N GLY A 712 " --> pdb=" O TYR A 705 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU A 737 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 591 removed outlier: 3.553A pdb=" N HIS A 578 " --> pdb=" O HIS A 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 552 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 554 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU A 601 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 623 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 659 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 621 " --> pdb=" O VAL A 659 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU A 601 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 642 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 678 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 829 through 831 Processing sheet with id=AB4, first strand: chain 'A' and resid 843 through 844 removed outlier: 6.089A pdb=" N THR A 843 " --> pdb=" O VAL C 935 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 862 through 864 Processing sheet with id=AB6, first strand: chain 'A' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY A1232 " --> pdb=" O SER A1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER A1228 " --> pdb=" O GLY A1232 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A1234 " --> pdb=" O VAL A1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A1226 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE A1236 " --> pdb=" O SER A1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A1224 " --> pdb=" O PHE A1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR A1238 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AB8, first strand: chain 'A' and resid 934 through 935 Processing sheet with id=AB9, first strand: chain 'A' and resid 1296 through 1299 Processing sheet with id=AC1, first strand: chain 'A' and resid 1269 through 1273 Processing sheet with id=AC2, first strand: chain 'B' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA B 227 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 107 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 124 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 151 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 180 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN B 199 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL B 312 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN B 482 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 320 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B 480 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS B 322 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 478 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 447 " --> pdb=" O TYR B 454 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL B 312 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN B 482 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 320 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B 480 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS B 322 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 478 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP B 485 " --> pdb=" O TYR B 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR B 500 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET B 487 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU B 498 " --> pdb=" O MET B 487 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP B 489 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA B 334 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 383 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 386 through 387 removed outlier: 5.796A pdb=" N TYR B 413 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE B 431 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS B 415 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 427 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE B 770 " --> pdb=" O GLN B 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 809 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 771 " --> pdb=" O TYR B 807 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 807 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 534 through 537 removed outlier: 3.504A pdb=" N GLY B 712 " --> pdb=" O TYR B 705 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU B 737 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 588 through 591 removed outlier: 3.552A pdb=" N HIS B 578 " --> pdb=" O HIS B 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 552 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 554 " --> pdb=" O THR B 608 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU B 601 " --> pdb=" O THR B 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 623 " --> pdb=" O SER B 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 659 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 621 " --> pdb=" O VAL B 659 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU B 601 " --> pdb=" O THR B 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 642 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 678 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 829 through 831 Processing sheet with id=AD5, first strand: chain 'B' and resid 862 through 864 Processing sheet with id=AD6, first strand: chain 'B' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY B1232 " --> pdb=" O SER B1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER B1228 " --> pdb=" O GLY B1232 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B1234 " --> pdb=" O VAL B1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B1226 " --> pdb=" O LEU B1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE B1236 " --> pdb=" O SER B1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B1224 " --> pdb=" O PHE B1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR B1238 " --> pdb=" O LEU B1222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 885 through 887 Processing sheet with id=AD8, first strand: chain 'B' and resid 934 through 935 Processing sheet with id=AD9, first strand: chain 'B' and resid 1296 through 1299 Processing sheet with id=AE1, first strand: chain 'B' and resid 1269 through 1273 Processing sheet with id=AE2, first strand: chain 'C' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA C 227 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C 107 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 124 " --> pdb=" O SER C 228 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 151 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C 180 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN C 199 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL C 312 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN C 482 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 320 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR C 480 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS C 322 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 478 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE C 447 " --> pdb=" O TYR C 454 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL C 312 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN C 482 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 320 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR C 480 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS C 322 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 478 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP C 485 " --> pdb=" O TYR C 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR C 500 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET C 487 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 498 " --> pdb=" O MET C 487 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP C 489 " --> pdb=" O THR C 496 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA C 334 " --> pdb=" O PHE C 465 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 383 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 386 through 387 removed outlier: 5.797A pdb=" N TYR C 413 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE C 431 " --> pdb=" O TYR C 413 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS C 415 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 427 " --> pdb=" O ALA C 417 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE C 770 " --> pdb=" O GLN C 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 809 " --> pdb=" O ALA C 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 771 " --> pdb=" O TYR C 807 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 807 " --> pdb=" O THR C 771 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 534 through 537 removed outlier: 3.503A pdb=" N GLY C 712 " --> pdb=" O TYR C 705 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU C 737 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 588 through 591 removed outlier: 3.553A pdb=" N HIS C 578 " --> pdb=" O HIS C 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 552 " --> pdb=" O LYS C 606 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 554 " --> pdb=" O THR C 608 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU C 601 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 623 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 659 " --> pdb=" O GLN C 621 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 621 " --> pdb=" O VAL C 659 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU C 601 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 642 " --> pdb=" O LYS C 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 678 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 829 through 831 Processing sheet with id=AF5, first strand: chain 'C' and resid 862 through 864 Processing sheet with id=AF6, first strand: chain 'C' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY C1232 " --> pdb=" O SER C1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER C1228 " --> pdb=" O GLY C1232 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C1234 " --> pdb=" O VAL C1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL C1226 " --> pdb=" O LEU C1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE C1236 " --> pdb=" O SER C1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER C1224 " --> pdb=" O PHE C1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C1238 " --> pdb=" O LEU C1222 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 885 through 887 Processing sheet with id=AF8, first strand: chain 'C' and resid 1296 through 1299 Processing sheet with id=AF9, first strand: chain 'C' and resid 1269 through 1273 875 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.26 Time building geometry restraints manager: 5.04 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: 9685 1.34 - 1.47: 9241 1.47 - 1.60: 13642 1.60 - 1.73: 0 1.73 - 1.86: 222 Bond restraints: 32790 Sorted by residual: bond pdb=" C3 NAG 3 1 " pdb=" C4 NAG 3 1 " ideal model delta sigma weight residual 1.524 1.455 0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C3 NAG l 1 " pdb=" C4 NAG l 1 " ideal model delta sigma weight residual 1.524 1.456 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C3 NAG T 1 " pdb=" C4 NAG T 1 " ideal model delta sigma weight residual 1.524 1.456 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" N LYS B 85 " pdb=" CA LYS B 85 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.26e-02 6.30e+03 9.13e+00 bond pdb=" N TYR B 253 " pdb=" CA TYR B 253 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 9.08e+00 ... (remaining 32785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 43580 3.35 - 6.71: 946 6.71 - 10.06: 127 10.06 - 13.42: 35 13.42 - 16.77: 15 Bond angle restraints: 44703 Sorted by residual: angle pdb=" C GLN C 775 " pdb=" N THR C 776 " pdb=" CA THR C 776 " ideal model delta sigma weight residual 120.87 110.35 10.52 1.42e+00 4.96e-01 5.49e+01 angle pdb=" C GLN A 775 " pdb=" N THR A 776 " pdb=" CA THR A 776 " ideal model delta sigma weight residual 120.87 110.35 10.52 1.42e+00 4.96e-01 5.48e+01 angle pdb=" C GLN B 775 " pdb=" N THR B 776 " pdb=" CA THR B 776 " ideal model delta sigma weight residual 120.87 110.37 10.50 1.42e+00 4.96e-01 5.47e+01 angle pdb=" C ASN A 774 " pdb=" CA ASN A 774 " pdb=" CB ASN A 774 " ideal model delta sigma weight residual 110.42 95.72 14.70 1.99e+00 2.53e-01 5.45e+01 angle pdb=" C ASN B 774 " pdb=" CA ASN B 774 " pdb=" CB ASN B 774 " ideal model delta sigma weight residual 110.42 95.73 14.69 1.99e+00 2.53e-01 5.45e+01 ... (remaining 44698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 15720 17.75 - 35.51: 1596 35.51 - 53.26: 207 53.26 - 71.01: 63 71.01 - 88.77: 27 Dihedral angle restraints: 17613 sinusoidal: 6654 harmonic: 10959 Sorted by residual: dihedral pdb=" C ASN A 774 " pdb=" N ASN A 774 " pdb=" CA ASN A 774 " pdb=" CB ASN A 774 " ideal model delta harmonic sigma weight residual -122.60 -99.83 -22.77 0 2.50e+00 1.60e-01 8.30e+01 dihedral pdb=" C ASN C 774 " pdb=" N ASN C 774 " pdb=" CA ASN C 774 " pdb=" CB ASN C 774 " ideal model delta harmonic sigma weight residual -122.60 -99.84 -22.76 0 2.50e+00 1.60e-01 8.29e+01 dihedral pdb=" C ASN B 774 " pdb=" N ASN B 774 " pdb=" CA ASN B 774 " pdb=" CB ASN B 774 " ideal model delta harmonic sigma weight residual -122.60 -99.84 -22.76 0 2.50e+00 1.60e-01 8.29e+01 ... (remaining 17610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 5703 0.310 - 0.619: 56 0.619 - 0.929: 13 0.929 - 1.239: 3 1.239 - 1.548: 3 Chirality restraints: 5778 Sorted by residual: chirality pdb=" C1 MAN T 6 " pdb=" O6 BMA T 3 " pdb=" C2 MAN T 6 " pdb=" O5 MAN T 6 " both_signs ideal model delta sigma weight residual False 2.40 0.85 1.55 2.00e-02 2.50e+03 5.99e+03 chirality pdb=" C1 MAN l 6 " pdb=" O6 BMA l 3 " pdb=" C2 MAN l 6 " pdb=" O5 MAN l 6 " both_signs ideal model delta sigma weight residual False 2.40 0.85 1.55 2.00e-02 2.50e+03 5.99e+03 chirality pdb=" C1 MAN 3 6 " pdb=" O6 BMA 3 3 " pdb=" C2 MAN 3 6 " pdb=" O5 MAN 3 6 " both_signs ideal model delta sigma weight residual False 2.40 0.86 1.54 2.00e-02 2.50e+03 5.95e+03 ... (remaining 5775 not shown) Planarity restraints: 5457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG M 2 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG e 2 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG e 2 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG e 2 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG e 2 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG w 2 " 0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG w 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG w 2 " 0.161 2.00e-02 2.50e+03 pdb=" N2 NAG w 2 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG w 2 " 0.104 2.00e-02 2.50e+03 ... (remaining 5454 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 847 2.65 - 3.21: 29237 3.21 - 3.78: 49006 3.78 - 4.34: 62037 4.34 - 4.90: 100985 Nonbonded interactions: 242112 Sorted by model distance: nonbonded pdb=" O3 NAG M 1 " pdb=" O7 NAG M 1 " model vdw 2.092 3.040 nonbonded pdb=" O3 NAG w 1 " pdb=" O7 NAG w 1 " model vdw 2.092 3.040 nonbonded pdb=" O3 NAG e 1 " pdb=" O7 NAG e 1 " model vdw 2.092 3.040 nonbonded pdb=" OD1 ASN B 254 " pdb=" OG1 THR B 256 " model vdw 2.172 3.040 nonbonded pdb=" OD1 ASN C 254 " pdb=" OG1 THR C 256 " model vdw 2.173 3.040 ... (remaining 242107 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: 0.08 Found NCS groups: ncs_group { reference = chain '0' selection = chain '4' selection = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = (chain '1' and resid 1 through 3) selection = (chain 'J' and resid 1 through 3) selection = (chain 'L' and resid 1 through 3) selection = (chain 'O' and resid 1 through 3) selection = (chain 'P' and resid 1 through 3) selection = (chain 'R' and resid 1 through 3) selection = (chain 'b' and resid 1 through 3) selection = (chain 'd' and resid 1 through 3) selection = (chain 'g' and resid 1 through 3) selection = (chain 'h' and resid 1 through 3) selection = (chain 'j' and resid 1 through 3) selection = (chain 't' and resid 1 through 3) selection = (chain 'v' and resid 1 through 3) selection = (chain 'y' and resid 1 through 3) selection = (chain 'z' and resid 1 through 3) } ncs_group { reference = chain '2' selection = chain 'S' selection = chain 'k' } ncs_group { reference = chain '3' selection = chain 'I' selection = chain 'T' selection = chain 'a' selection = chain 'l' selection = chain 's' } ncs_group { reference = (chain 'A' and (resid 62 through 1337 or resid 1522 through 1523 or resid 1536 t \ hrough 1572)) selection = (chain 'B' and (resid 62 through 1337 or resid 1522 through 1523 or resid 1536 t \ hrough 1572)) selection = (chain 'C' and (resid 62 through 1337 or resid 1509 through 1523 or resid 1536 t \ hrough 1570)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'o' selection = chain 'q' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.410 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: 0.710 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 33.830 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 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 : 0.011 0.574 33048 Z= 0.722 Angle : 1.427 25.948 45426 Z= 0.642 Chirality : 0.098 1.548 5778 Planarity : 0.020 0.299 5376 Dihedral : 14.573 88.768 10455 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.32 % Favored : 87.36 % Rotamer: Outliers : 0.82 % Allowed : 9.10 % Favored : 90.07 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.20 (0.10), residues: 3717 helix: -3.94 (0.08), residues: 729 sheet: -2.68 (0.16), residues: 906 loop : -3.75 (0.10), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1283 TYR 0.035 0.002 TYR B 826 PHE 0.016 0.002 PHE C 629 TRP 0.010 0.002 TRP A 200 HIS 0.010 0.002 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00967 / 0.47 (32790) covalent geometry : angle 1.26308 / 0.60 (44703) SS BOND : bond 0.00733 / 0.49 ( 42) SS BOND : angle 2.13244 / 1.54 ( 84) hydrogen bonds : bond 0.30914 / 20.86 ( 851) hydrogen bonds : angle 10.82716 / 7.54 ( 2427) Misc. bond : bond 0.57358 / 28.75 ( 3) link_ALPHA1-2 : bond 0.01071 / 0.66 ( 6) link_ALPHA1-2 : angle 4.81943 / 2.58 ( 18) link_ALPHA1-3 : bond 0.00719 / 0.36 ( 12) link_ALPHA1-3 : angle 5.08004 / 3.32 ( 36) link_ALPHA1-6 : bond 0.00636 / 0.41 ( 24) link_ALPHA1-6 : angle 4.08315 / 2.67 ( 72) link_BETA1-4 : bond 0.01090 / 0.72 ( 87) link_BETA1-4 : angle 5.16963 / 3.35 ( 261) link_BETA1-6 : bond 0.00188 / 0.09 ( 3) link_BETA1-6 : angle 2.02275 / 1.24 ( 9) link_NAG-ASN : bond 0.02247 / 1.58 ( 81) link_NAG-ASN : angle 6.81487 / 4.62 ( 243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 782 time to evaluate : 1.109 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: A 158 ASN cc_start: 0.2529 (OUTLIER) cc_final: 0.2141 (m-40) REVERT: A 309 GLN cc_start: 0.8763 (mt0) cc_final: 0.8439 (tt0) REVERT: A 341 ASP cc_start: 0.8068 (p0) cc_final: 0.6875 (p0) REVERT: A 444 ASP cc_start: 0.7505 (p0) cc_final: 0.7256 (p0) REVERT: A 461 LYS cc_start: 0.8293 (tttt) cc_final: 0.7940 (tmtt) REVERT: A 477 THR cc_start: 0.7415 (p) cc_final: 0.7141 (p) REVERT: A 592 THR cc_start: 0.8005 (p) cc_final: 0.7754 (t) REVERT: A 597 GLN cc_start: 0.8432 (mt0) cc_final: 0.8203 (mt0) REVERT: A 611 GLN cc_start: 0.8094 (pt0) cc_final: 0.7736 (pt0) REVERT: A 641 GLU cc_start: 0.7851 (tp30) cc_final: 0.7553 (tp30) REVERT: A 680 MET cc_start: 0.7596 (mmt) cc_final: 0.7081 (mtp) REVERT: A 701 GLU cc_start: 0.7856 (pt0) cc_final: 0.7289 (pm20) REVERT: A 702 CYS cc_start: 0.6646 (m) cc_final: 0.6373 (m) REVERT: A 803 MET cc_start: 0.8738 (mmm) cc_final: 0.8416 (mmm) REVERT: A 812 TRP cc_start: 0.7001 (p-90) cc_final: 0.6465 (p-90) REVERT: A 824 ILE cc_start: 0.8488 (mm) cc_final: 0.8212 (tp) REVERT: A 898 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7527 (ttp80) REVERT: A 928 MET cc_start: 0.7900 (tpp) cc_final: 0.7423 (tpp) REVERT: A 973 ARG cc_start: 0.6400 (mtt180) cc_final: 0.6131 (mtp85) REVERT: A 1059 MET cc_start: 0.8265 (ttm) cc_final: 0.7888 (ttm) REVERT: A 1067 TYR cc_start: 0.8552 (m-80) cc_final: 0.8340 (m-10) REVERT: A 1076 GLN cc_start: 0.7390 (mm-40) cc_final: 0.6768 (tp40) REVERT: A 1141 LYS cc_start: 0.8210 (mttt) cc_final: 0.7915 (mtpt) REVERT: A 1152 GLU cc_start: 0.7675 (tp30) cc_final: 0.7269 (tp30) REVERT: A 1155 ASN cc_start: 0.8715 (m-40) cc_final: 0.8213 (m-40) REVERT: A 1159 LYS cc_start: 0.8380 (tttt) cc_final: 0.8097 (ttmt) REVERT: A 1260 TYR cc_start: 0.7422 (m-80) cc_final: 0.7068 (m-10) REVERT: A 1279 MET cc_start: 0.7451 (mmm) cc_final: 0.7236 (mmt) REVERT: A 1315 GLN cc_start: 0.7542 (mp10) cc_final: 0.7175 (tm-30) REVERT: A 1331 MET cc_start: 0.6853 (mpp) cc_final: 0.6578 (tmm) REVERT: B 158 ASN cc_start: 0.2839 (OUTLIER) cc_final: 0.2425 (m-40) REVERT: B 592 THR cc_start: 0.8093 (p) cc_final: 0.7829 (t) REVERT: B 611 GLN cc_start: 0.8083 (pt0) cc_final: 0.7700 (pt0) REVERT: B 633 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7982 (mm-40) REVERT: B 680 MET cc_start: 0.7803 (mmt) cc_final: 0.7285 (mtp) REVERT: B 701 GLU cc_start: 0.7783 (pt0) cc_final: 0.7215 (pm20) REVERT: B 702 CYS cc_start: 0.6816 (m) cc_final: 0.6448 (m) REVERT: B 803 MET cc_start: 0.8706 (mmm) cc_final: 0.8296 (mmm) REVERT: B 824 ILE cc_start: 0.8461 (mm) cc_final: 0.8086 (tp) REVERT: B 883 LYS cc_start: 0.8646 (mttm) cc_final: 0.8342 (mttm) REVERT: B 928 MET cc_start: 0.7869 (tpp) cc_final: 0.7572 (tpp) REVERT: B 973 ARG cc_start: 0.6383 (mtt180) cc_final: 0.6060 (mtp85) REVERT: B 1011 ASP cc_start: 0.6372 (t0) cc_final: 0.6050 (t0) REVERT: B 1059 MET cc_start: 0.8184 (ttm) cc_final: 0.7757 (ttm) REVERT: B 1076 GLN cc_start: 0.7342 (mm-40) cc_final: 0.6631 (tp-100) REVERT: B 1155 ASN cc_start: 0.8718 (m-40) cc_final: 0.8148 (m-40) REVERT: B 1159 LYS cc_start: 0.8310 (tttt) cc_final: 0.8108 (mttt) REVERT: B 1161 GLU cc_start: 0.6639 (pm20) cc_final: 0.6404 (pm20) REVERT: B 1283 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7366 (mtm-85) REVERT: B 1307 LEU cc_start: 0.8270 (tp) cc_final: 0.8051 (tt) REVERT: B 1315 GLN cc_start: 0.7678 (mp10) cc_final: 0.7205 (tm-30) REVERT: B 1319 ILE cc_start: 0.7309 (tt) cc_final: 0.7094 (pt) REVERT: C 158 ASN cc_start: 0.2821 (OUTLIER) cc_final: 0.2430 (m110) REVERT: C 364 TYR cc_start: 0.8266 (m-10) cc_final: 0.7895 (m-80) REVERT: C 444 ASP cc_start: 0.7428 (p0) cc_final: 0.7159 (p0) REVERT: C 455 PHE cc_start: 0.8290 (p90) cc_final: 0.8079 (p90) REVERT: C 571 LEU cc_start: 0.7110 (mp) cc_final: 0.6868 (mp) REVERT: C 592 THR cc_start: 0.8001 (p) cc_final: 0.7757 (t) REVERT: C 611 GLN cc_start: 0.8069 (pt0) cc_final: 0.7689 (pt0) REVERT: C 623 GLN cc_start: 0.7844 (mt0) cc_final: 0.7420 (mt0) REVERT: C 641 GLU cc_start: 0.7724 (tp30) cc_final: 0.7497 (tp30) REVERT: C 668 PHE cc_start: 0.8064 (m-10) cc_final: 0.7851 (m-10) REVERT: C 680 MET cc_start: 0.7682 (mmt) cc_final: 0.7092 (mtp) REVERT: C 701 GLU cc_start: 0.7746 (pt0) cc_final: 0.7253 (pm20) REVERT: C 702 CYS cc_start: 0.6689 (m) cc_final: 0.6211 (m) REVERT: C 803 MET cc_start: 0.8612 (mmm) cc_final: 0.8118 (mmm) REVERT: C 883 LYS cc_start: 0.8569 (mttm) cc_final: 0.8248 (mttm) REVERT: C 898 ARG cc_start: 0.7739 (ttp80) cc_final: 0.6963 (tpp80) REVERT: C 902 ASN cc_start: 0.8529 (m-40) cc_final: 0.8312 (m-40) REVERT: C 928 MET cc_start: 0.7867 (tpp) cc_final: 0.7431 (tpp) REVERT: C 973 ARG cc_start: 0.6274 (mtt180) cc_final: 0.6033 (mtp85) REVERT: C 1059 MET cc_start: 0.8118 (ttm) cc_final: 0.7787 (ttm) REVERT: C 1076 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6626 (tp40) REVERT: C 1084 ASN cc_start: 0.8592 (m-40) cc_final: 0.8375 (m-40) REVERT: C 1141 LYS cc_start: 0.8132 (mttt) cc_final: 0.7908 (mtmt) REVERT: C 1155 ASN cc_start: 0.8664 (m-40) cc_final: 0.7418 (t0) REVERT: C 1159 LYS cc_start: 0.8312 (tttt) cc_final: 0.7922 (tttt) REVERT: C 1283 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7049 (mtm-85) REVERT: C 1293 MET cc_start: 0.8211 (pmm) cc_final: 0.7989 (tpp) REVERT: C 1307 LEU cc_start: 0.8390 (tp) cc_final: 0.8176 (tt) REVERT: C 1315 GLN cc_start: 0.7586 (mp10) cc_final: 0.7178 (tm-30) REVERT: C 1331 MET cc_start: 0.6848 (mpp) cc_final: 0.6422 (tpt) outliers start: 27 outliers final: 9 residues processed: 807 average time/residue: 0.2006 time to fit residues: 266.7532 Evaluate side-chains 558 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 546 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 595 CYS Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 595 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN A 93 ASN A 95 ASN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 220 ASN A 418 ASN A 611 GLN A 623 GLN A 660 HIS A 667 GLN A1122 GLN A1126 ASN A1311 HIS B 83 ASN B 93 ASN B 95 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 177 GLN B 220 ASN B 418 ASN B 450 ASN B 551 HIS B 611 GLN B 623 GLN B 660 HIS B 667 GLN B1122 GLN B1126 ASN ** B1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN C 83 ASN C 93 ASN C 95 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 177 GLN C 220 ASN C 372 GLN C 411 ASN C 611 GLN C 623 GLN C 624 ASN C 660 HIS C 667 GLN C 758 GLN C 986 ASN C1122 GLN C1126 ASN ** C1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115929 restraints weight = 51314.342| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 4.21 r_work: 0.3265 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33048 Z= 0.182 Angle : 0.933 14.386 45426 Z= 0.423 Chirality : 0.052 0.408 5778 Planarity : 0.004 0.054 5376 Dihedral : 7.091 36.692 4032 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.25 % Favored : 88.67 % Rotamer: Outliers : 2.63 % Allowed : 14.48 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.33 % 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: -4.05 (0.12), residues: 3717 helix: -1.45 (0.16), residues: 759 sheet: -2.35 (0.16), residues: 882 loop : -3.47 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1283 TYR 0.025 0.001 TYR A 204 PHE 0.027 0.001 PHE B 428 TRP 0.021 0.001 TRP B 812 HIS 0.007 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (32790) covalent geometry : angle 0.83564 / 0.40 (44703) SS BOND : bond 0.00580 / 0.35 ( 42) SS BOND : angle 1.68222 / 1.21 ( 84) hydrogen bonds : bond 0.05991 / 4.16 ( 851) hydrogen bonds : angle 6.48835 / 4.47 ( 2427) Misc. bond : bond 0.00078 / 0.04 ( 3) link_ALPHA1-2 : bond 0.02013 / 0.97 ( 6) link_ALPHA1-2 : angle 3.29841 / 1.69 ( 18) link_ALPHA1-3 : bond 0.01037 / 0.48 ( 12) link_ALPHA1-3 : angle 3.76010 / 2.36 ( 36) link_ALPHA1-6 : bond 0.01533 / 1.01 ( 24) link_ALPHA1-6 : angle 2.26632 / 1.58 ( 72) link_BETA1-4 : bond 0.01179 / 0.83 ( 87) link_BETA1-4 : angle 3.04858 / 2.12 ( 261) link_BETA1-6 : bond 0.00305 / 0.15 ( 3) link_BETA1-6 : angle 1.36447 / 0.86 ( 9) link_NAG-ASN : bond 0.00709 / 0.48 ( 81) link_NAG-ASN : angle 4.33544 / 2.76 ( 243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 653 time to evaluate : 1.222 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: A 309 GLN cc_start: 0.9061 (mt0) cc_final: 0.8854 (tt0) REVERT: A 461 LYS cc_start: 0.8858 (tttt) cc_final: 0.8548 (tttm) REVERT: A 471 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7175 (tp30) REVERT: A 516 GLU cc_start: 0.8215 (tp30) cc_final: 0.8002 (tp30) REVERT: A 592 THR cc_start: 0.8146 (p) cc_final: 0.7872 (t) REVERT: A 595 CYS cc_start: 0.6827 (t) cc_final: 0.6585 (t) REVERT: A 641 GLU cc_start: 0.8361 (tp30) cc_final: 0.7945 (tp30) REVERT: A 680 MET cc_start: 0.8083 (mmt) cc_final: 0.7519 (mtp) REVERT: A 701 GLU cc_start: 0.8271 (pt0) cc_final: 0.7829 (pm20) REVERT: A 702 CYS cc_start: 0.8022 (m) cc_final: 0.7783 (m) REVERT: A 775 GLN cc_start: 0.8533 (pm20) cc_final: 0.8000 (pm20) REVERT: A 803 MET cc_start: 0.8954 (mmm) cc_final: 0.8499 (mmm) REVERT: A 812 TRP cc_start: 0.7250 (p-90) cc_final: 0.7043 (p-90) REVERT: A 824 ILE cc_start: 0.8770 (mm) cc_final: 0.8505 (tp) REVERT: A 829 PHE cc_start: 0.7456 (m-80) cc_final: 0.6825 (p90) REVERT: A 883 LYS cc_start: 0.9079 (mmtp) cc_final: 0.8853 (mmtp) REVERT: A 898 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7464 (tpp80) REVERT: A 928 MET cc_start: 0.8461 (tpp) cc_final: 0.8221 (tpt) REVERT: A 973 ARG cc_start: 0.7009 (mtt180) cc_final: 0.6626 (mtp85) REVERT: A 1033 MET cc_start: 0.8869 (tpp) cc_final: 0.8663 (mmm) REVERT: A 1059 MET cc_start: 0.8671 (ttm) cc_final: 0.8424 (ttm) REVERT: A 1076 GLN cc_start: 0.7439 (mm-40) cc_final: 0.6881 (tp40) REVERT: A 1141 LYS cc_start: 0.8806 (mttt) cc_final: 0.8446 (mtpt) REVERT: A 1152 GLU cc_start: 0.8348 (tp30) cc_final: 0.7806 (tp30) REVERT: A 1155 ASN cc_start: 0.8828 (m-40) cc_final: 0.7717 (t0) REVERT: A 1260 TYR cc_start: 0.7715 (m-80) cc_final: 0.7494 (m-10) REVERT: A 1279 MET cc_start: 0.8183 (mmm) cc_final: 0.7974 (mmt) REVERT: A 1315 GLN cc_start: 0.7541 (mp10) cc_final: 0.7224 (tm-30) REVERT: B 286 ASP cc_start: 0.8679 (t0) cc_final: 0.8429 (t0) REVERT: B 455 PHE cc_start: 0.8433 (p90) cc_final: 0.8125 (p90) REVERT: B 570 GLU cc_start: 0.7504 (mp0) cc_final: 0.7301 (tp30) REVERT: B 592 THR cc_start: 0.8263 (p) cc_final: 0.7971 (t) REVERT: B 595 CYS cc_start: 0.6778 (t) cc_final: 0.6483 (t) REVERT: B 633 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8203 (mm-40) REVERT: B 641 GLU cc_start: 0.8281 (tp30) cc_final: 0.7485 (tp30) REVERT: B 680 MET cc_start: 0.8215 (mmt) cc_final: 0.7582 (mtp) REVERT: B 701 GLU cc_start: 0.8218 (pt0) cc_final: 0.7776 (pm20) REVERT: B 702 CYS cc_start: 0.8159 (m) cc_final: 0.7835 (m) REVERT: B 775 GLN cc_start: 0.8578 (pm20) cc_final: 0.8014 (pm20) REVERT: B 803 MET cc_start: 0.8986 (mmm) cc_final: 0.8762 (mmp) REVERT: B 824 ILE cc_start: 0.8782 (mm) cc_final: 0.8385 (tp) REVERT: B 829 PHE cc_start: 0.7380 (m-80) cc_final: 0.6895 (p90) REVERT: B 898 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7341 (tpp80) REVERT: B 928 MET cc_start: 0.8396 (tpp) cc_final: 0.7877 (tpp) REVERT: B 973 ARG cc_start: 0.7002 (mtt180) cc_final: 0.6637 (mtp85) REVERT: B 1059 MET cc_start: 0.8569 (ttm) cc_final: 0.8254 (ttm) REVERT: B 1076 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6729 (tp-100) REVERT: B 1155 ASN cc_start: 0.8804 (m-40) cc_final: 0.7884 (t0) REVERT: B 1161 GLU cc_start: 0.7357 (pm20) cc_final: 0.6996 (pm20) REVERT: B 1283 ARG cc_start: 0.8902 (mtt90) cc_final: 0.7929 (mtm180) REVERT: B 1307 LEU cc_start: 0.8463 (tp) cc_final: 0.8222 (tt) REVERT: B 1321 TYR cc_start: 0.8291 (t80) cc_final: 0.7986 (t80) REVERT: C 158 ASN cc_start: 0.2399 (OUTLIER) cc_final: 0.2158 (m-40) REVERT: C 198 PHE cc_start: 0.8544 (m-10) cc_final: 0.8228 (m-10) REVERT: C 286 ASP cc_start: 0.8569 (t0) cc_final: 0.8321 (t0) REVERT: C 455 PHE cc_start: 0.8421 (p90) cc_final: 0.8187 (p90) REVERT: C 571 LEU cc_start: 0.7548 (mp) cc_final: 0.7326 (mp) REVERT: C 592 THR cc_start: 0.8155 (p) cc_final: 0.7900 (t) REVERT: C 595 CYS cc_start: 0.6925 (t) cc_final: 0.6646 (t) REVERT: C 623 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8213 (mt0) REVERT: C 702 CYS cc_start: 0.8031 (m) cc_final: 0.7629 (m) REVERT: C 775 GLN cc_start: 0.8531 (pm20) cc_final: 0.8002 (pm20) REVERT: C 803 MET cc_start: 0.8989 (mmm) cc_final: 0.8404 (mmm) REVERT: C 805 GLN cc_start: 0.8615 (mt0) cc_final: 0.8097 (mp10) REVERT: C 829 PHE cc_start: 0.7390 (m-80) cc_final: 0.6758 (p90) REVERT: C 883 LYS cc_start: 0.9130 (mttm) cc_final: 0.8852 (mmtp) REVERT: C 898 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7330 (tpp80) REVERT: C 928 MET cc_start: 0.8520 (tpp) cc_final: 0.8218 (tpt) REVERT: C 973 ARG cc_start: 0.6966 (mtt180) cc_final: 0.6601 (mtp85) REVERT: C 986 ASN cc_start: 0.8204 (m-40) cc_final: 0.7920 (m110) REVERT: C 1000 TYR cc_start: 0.8492 (m-80) cc_final: 0.8055 (m-80) REVERT: C 1076 GLN cc_start: 0.7388 (mm-40) cc_final: 0.6702 (tp40) REVERT: C 1141 LYS cc_start: 0.8715 (mttt) cc_final: 0.8433 (mtmt) REVERT: C 1152 GLU cc_start: 0.8338 (tp30) cc_final: 0.7636 (tp30) REVERT: C 1155 ASN cc_start: 0.8855 (m-40) cc_final: 0.7901 (t0) REVERT: C 1159 LYS cc_start: 0.8678 (tttt) cc_final: 0.8386 (tttt) REVERT: C 1279 MET cc_start: 0.8283 (mmt) cc_final: 0.8066 (mmt) REVERT: C 1307 LEU cc_start: 0.8489 (tp) cc_final: 0.8186 (tt) REVERT: C 1315 GLN cc_start: 0.7664 (mp10) cc_final: 0.7274 (tm-30) REVERT: C 1331 MET cc_start: 0.6504 (mpp) cc_final: 0.6124 (tpt) outliers start: 86 outliers final: 51 residues processed: 711 average time/residue: 0.1886 time to fit residues: 226.5689 Evaluate side-chains 606 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 553 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1238 THR Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 623 GLN Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1309 THR Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 191 optimal weight: 3.9990 chunk 48 optimal weight: 0.0570 chunk 315 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 341 optimal weight: 0.2980 chunk 174 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 147 optimal weight: 0.3980 chunk 134 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 overall best weight: 0.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS A 583 GLN A 623 GLN A 758 GLN A 763 ASN B 83 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN B 583 GLN B 623 GLN B 758 GLN B 763 ASN B1227 ASN ** B1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN C 515 HIS C 583 GLN C 611 GLN C 623 GLN C 763 ASN ** C1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117180 restraints weight = 51220.258| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.17 r_work: 0.3296 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33048 Z= 0.130 Angle : 0.820 14.429 45426 Z= 0.370 Chirality : 0.049 0.369 5778 Planarity : 0.004 0.048 5376 Dihedral : 6.426 32.595 4023 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 3.30 % Allowed : 16.68 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -3.45 (0.12), residues: 3717 helix: -0.26 (0.18), residues: 768 sheet: -2.08 (0.16), residues: 924 loop : -3.34 (0.11), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 977 TYR 0.021 0.001 TYR C 204 PHE 0.038 0.001 PHE A 104 TRP 0.023 0.001 TRP A 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (32790) covalent geometry : angle 0.72360 / 0.35 (44703) SS BOND : bond 0.00420 / 0.27 ( 42) SS BOND : angle 1.52060 / 1.08 ( 84) hydrogen bonds : bond 0.04438 / 3.11 ( 851) hydrogen bonds : angle 5.71666 / 3.92 ( 2427) Misc. bond : bond 0.00313 / 0.16 ( 3) link_ALPHA1-2 : bond 0.01455 / 0.71 ( 6) link_ALPHA1-2 : angle 2.93764 / 1.46 ( 18) link_ALPHA1-3 : bond 0.00651 / 0.30 ( 12) link_ALPHA1-3 : angle 3.65658 / 2.30 ( 36) link_ALPHA1-6 : bond 0.01321 / 0.88 ( 24) link_ALPHA1-6 : angle 1.97400 / 1.37 ( 72) link_BETA1-4 : bond 0.01046 / 0.74 ( 87) link_BETA1-4 : angle 2.71449 / 1.87 ( 261) link_BETA1-6 : bond 0.00358 / 0.18 ( 3) link_BETA1-6 : angle 1.25112 / 0.79 ( 9) link_NAG-ASN : bond 0.00692 / 0.46 ( 81) link_NAG-ASN : angle 4.08696 / 2.59 ( 243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 601 time to evaluate : 1.356 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: A 115 TRP cc_start: 0.7238 (p-90) cc_final: 0.6931 (p-90) REVERT: A 286 ASP cc_start: 0.8496 (t0) cc_final: 0.8198 (t0) REVERT: A 309 GLN cc_start: 0.9159 (mt0) cc_final: 0.8941 (tt0) REVERT: A 371 ASP cc_start: 0.7101 (p0) cc_final: 0.6301 (m-30) REVERT: A 372 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8662 (tt0) REVERT: A 382 THR cc_start: 0.7834 (m) cc_final: 0.7516 (t) REVERT: A 461 LYS cc_start: 0.8807 (tttt) cc_final: 0.8512 (tttm) REVERT: A 597 GLN cc_start: 0.8428 (mt0) cc_final: 0.8025 (tt0) REVERT: A 641 GLU cc_start: 0.8276 (tp30) cc_final: 0.7891 (tp30) REVERT: A 664 TRP cc_start: 0.6750 (m-10) cc_final: 0.6267 (m100) REVERT: A 680 MET cc_start: 0.8067 (mmt) cc_final: 0.7458 (mtp) REVERT: A 702 CYS cc_start: 0.7922 (m) cc_final: 0.7661 (m) REVERT: A 824 ILE cc_start: 0.8706 (mm) cc_final: 0.8418 (tp) REVERT: A 829 PHE cc_start: 0.7474 (m-80) cc_final: 0.6775 (p90) REVERT: A 898 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7357 (tpp80) REVERT: A 928 MET cc_start: 0.8412 (tpp) cc_final: 0.7935 (tpp) REVERT: A 973 ARG cc_start: 0.6712 (mtt180) cc_final: 0.6343 (mtp85) REVERT: A 1000 TYR cc_start: 0.8509 (m-80) cc_final: 0.8172 (m-80) REVERT: A 1059 MET cc_start: 0.8620 (ttm) cc_final: 0.8376 (ttm) REVERT: A 1141 LYS cc_start: 0.8785 (mttt) cc_final: 0.8428 (mtpt) REVERT: A 1152 GLU cc_start: 0.8296 (tp30) cc_final: 0.7632 (tp30) REVERT: A 1155 ASN cc_start: 0.8656 (m-40) cc_final: 0.7534 (t0) REVERT: A 1260 TYR cc_start: 0.7654 (m-80) cc_final: 0.7368 (m-10) REVERT: A 1279 MET cc_start: 0.8083 (mmm) cc_final: 0.7857 (mmt) REVERT: A 1290 LYS cc_start: 0.8812 (mttt) cc_final: 0.8527 (mttp) REVERT: B 247 ARG cc_start: 0.7437 (mtt180) cc_final: 0.6819 (mtt90) REVERT: B 286 ASP cc_start: 0.8727 (t70) cc_final: 0.8282 (t0) REVERT: B 293 PHE cc_start: 0.8865 (t80) cc_final: 0.8544 (t80) REVERT: B 382 THR cc_start: 0.7996 (m) cc_final: 0.7676 (t) REVERT: B 603 LEU cc_start: 0.8925 (tp) cc_final: 0.8611 (tp) REVERT: B 633 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7976 (mm-40) REVERT: B 641 GLU cc_start: 0.8273 (tp30) cc_final: 0.7672 (tp30) REVERT: B 663 LYS cc_start: 0.8737 (tttt) cc_final: 0.8488 (tppp) REVERT: B 664 TRP cc_start: 0.6841 (m-10) cc_final: 0.6384 (m100) REVERT: B 680 MET cc_start: 0.8194 (mmt) cc_final: 0.7520 (mtp) REVERT: B 702 CYS cc_start: 0.8093 (m) cc_final: 0.7747 (m) REVERT: B 775 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: B 803 MET cc_start: 0.8893 (mmm) cc_final: 0.8670 (mmp) REVERT: B 822 SER cc_start: 0.8683 (m) cc_final: 0.8470 (t) REVERT: B 824 ILE cc_start: 0.8777 (mm) cc_final: 0.8346 (tp) REVERT: B 829 PHE cc_start: 0.7335 (m-80) cc_final: 0.6821 (p90) REVERT: B 898 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7241 (tpp80) REVERT: B 928 MET cc_start: 0.8311 (tpp) cc_final: 0.7851 (tpp) REVERT: B 973 ARG cc_start: 0.6987 (mtt180) cc_final: 0.6634 (mtp85) REVERT: B 982 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: B 1059 MET cc_start: 0.8495 (ttm) cc_final: 0.8194 (ttm) REVERT: B 1066 ASN cc_start: 0.8835 (m-40) cc_final: 0.8430 (m110) REVERT: B 1152 GLU cc_start: 0.8361 (tp30) cc_final: 0.7610 (tp30) REVERT: B 1155 ASN cc_start: 0.8683 (m-40) cc_final: 0.7789 (t0) REVERT: B 1161 GLU cc_start: 0.7311 (pm20) cc_final: 0.6976 (pm20) REVERT: B 1283 ARG cc_start: 0.8904 (mtt90) cc_final: 0.7922 (mtm180) REVERT: B 1293 MET cc_start: 0.8383 (tpt) cc_final: 0.8182 (tpt) REVERT: B 1307 LEU cc_start: 0.8428 (tp) cc_final: 0.8162 (tt) REVERT: C 286 ASP cc_start: 0.8697 (t0) cc_final: 0.8193 (t0) REVERT: C 382 THR cc_start: 0.7972 (m) cc_final: 0.7720 (t) REVERT: C 623 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: C 663 LYS cc_start: 0.8744 (tttt) cc_final: 0.8522 (tppp) REVERT: C 664 TRP cc_start: 0.6770 (m-10) cc_final: 0.6305 (m100) REVERT: C 680 MET cc_start: 0.7934 (mmt) cc_final: 0.7411 (mtp) REVERT: C 701 GLU cc_start: 0.8180 (pt0) cc_final: 0.7780 (pm20) REVERT: C 702 CYS cc_start: 0.7906 (m) cc_final: 0.7509 (m) REVERT: C 805 GLN cc_start: 0.8533 (mt0) cc_final: 0.8067 (mp10) REVERT: C 829 PHE cc_start: 0.7395 (m-80) cc_final: 0.6811 (p90) REVERT: C 883 LYS cc_start: 0.9118 (mttm) cc_final: 0.8864 (mmtp) REVERT: C 898 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7283 (tpp80) REVERT: C 928 MET cc_start: 0.8465 (tpp) cc_final: 0.7753 (tpp) REVERT: C 938 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8068 (tpm-80) REVERT: C 973 ARG cc_start: 0.6905 (mtt180) cc_final: 0.6589 (mtp85) REVERT: C 986 ASN cc_start: 0.8113 (m-40) cc_final: 0.7891 (m110) REVERT: C 1066 ASN cc_start: 0.8795 (m-40) cc_final: 0.8360 (m110) REVERT: C 1141 LYS cc_start: 0.8673 (mttt) cc_final: 0.8352 (mtmt) REVERT: C 1152 GLU cc_start: 0.8259 (tp30) cc_final: 0.7503 (tp30) REVERT: C 1155 ASN cc_start: 0.8781 (m-40) cc_final: 0.7794 (t0) REVERT: C 1268 ASP cc_start: 0.8676 (m-30) cc_final: 0.8437 (m-30) REVERT: C 1279 MET cc_start: 0.8200 (mmt) cc_final: 0.7955 (mmt) REVERT: C 1307 LEU cc_start: 0.8282 (tp) cc_final: 0.8017 (tt) REVERT: C 1331 MET cc_start: 0.6527 (mpp) cc_final: 0.6197 (tpt) outliers start: 108 outliers final: 57 residues processed: 673 average time/residue: 0.1904 time to fit residues: 217.6831 Evaluate side-chains 610 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 548 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1227 ASN Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 623 GLN Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 49 optimal weight: 10.0000 chunk 326 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 332 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN A 109 HIS ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS A1078 ASN B 109 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1066 ASN B1078 ASN C 109 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 623 GLN C1066 ASN C1078 ASN C1311 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.156515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114355 restraints weight = 51149.127| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.87 r_work: 0.3249 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33048 Z= 0.180 Angle : 0.817 13.967 45426 Z= 0.372 Chirality : 0.049 0.363 5778 Planarity : 0.004 0.047 5376 Dihedral : 6.169 31.108 4014 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 4.67 % Allowed : 16.80 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.14 (0.13), residues: 3717 helix: 0.32 (0.19), residues: 750 sheet: -2.03 (0.16), residues: 930 loop : -3.18 (0.12), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 977 TYR 0.025 0.002 TYR B1067 PHE 0.041 0.001 PHE B 104 TRP 0.021 0.001 TRP B 222 HIS 0.005 0.001 HIS C 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (32790) covalent geometry : angle 0.72539 / 0.35 (44703) SS BOND : bond 0.00392 / 0.25 ( 42) SS BOND : angle 1.39679 / 1.05 ( 84) hydrogen bonds : bond 0.04167 / 2.92 ( 851) hydrogen bonds : angle 5.36363 / 3.69 ( 2427) Misc. bond : bond 0.00086 / 0.04 ( 3) link_ALPHA1-2 : bond 0.01224 / 0.60 ( 6) link_ALPHA1-2 : angle 2.55564 / 1.29 ( 18) link_ALPHA1-3 : bond 0.00653 / 0.30 ( 12) link_ALPHA1-3 : angle 3.59999 / 2.27 ( 36) link_ALPHA1-6 : bond 0.01061 / 0.70 ( 24) link_ALPHA1-6 : angle 1.83928 / 1.27 ( 72) link_BETA1-4 : bond 0.00996 / 0.70 ( 87) link_BETA1-4 : angle 2.72387 / 1.89 ( 261) link_BETA1-6 : bond 0.00321 / 0.16 ( 3) link_BETA1-6 : angle 1.20777 / 0.76 ( 9) link_NAG-ASN : bond 0.00642 / 0.43 ( 81) link_NAG-ASN : angle 3.97306 / 2.52 ( 243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 592 time to evaluate : 1.205 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: A 115 TRP cc_start: 0.7361 (p-90) cc_final: 0.7056 (p-90) REVERT: A 245 VAL cc_start: 0.8600 (t) cc_final: 0.8269 (t) REVERT: A 247 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7392 (mtm110) REVERT: A 286 ASP cc_start: 0.8572 (t70) cc_final: 0.8299 (t0) REVERT: A 371 ASP cc_start: 0.7119 (p0) cc_final: 0.6369 (m-30) REVERT: A 372 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: A 382 THR cc_start: 0.8013 (m) cc_final: 0.7683 (t) REVERT: A 461 LYS cc_start: 0.8865 (tttt) cc_final: 0.8554 (tttm) REVERT: A 477 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7472 (p) REVERT: A 597 GLN cc_start: 0.8414 (mt0) cc_final: 0.8136 (tt0) REVERT: A 641 GLU cc_start: 0.8316 (tp30) cc_final: 0.8105 (tp30) REVERT: A 664 TRP cc_start: 0.6771 (m-10) cc_final: 0.6395 (m100) REVERT: A 680 MET cc_start: 0.8164 (mmt) cc_final: 0.7661 (mtp) REVERT: A 701 GLU cc_start: 0.8267 (pt0) cc_final: 0.7825 (pm20) REVERT: A 702 CYS cc_start: 0.7925 (m) cc_final: 0.7650 (m) REVERT: A 824 ILE cc_start: 0.8750 (mm) cc_final: 0.8474 (tp) REVERT: A 829 PHE cc_start: 0.7412 (m-80) cc_final: 0.6863 (p90) REVERT: A 898 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7386 (tpp80) REVERT: A 928 MET cc_start: 0.8443 (tpp) cc_final: 0.7913 (tpp) REVERT: A 973 ARG cc_start: 0.6844 (mtt180) cc_final: 0.6455 (mtp85) REVERT: A 1059 MET cc_start: 0.8657 (ttm) cc_final: 0.8412 (ttm) REVERT: A 1067 TYR cc_start: 0.8778 (m-80) cc_final: 0.8466 (m-10) REVERT: A 1076 GLN cc_start: 0.7909 (mp10) cc_final: 0.6966 (tp40) REVERT: A 1141 LYS cc_start: 0.8839 (mttt) cc_final: 0.8394 (mtpt) REVERT: A 1152 GLU cc_start: 0.8325 (tp30) cc_final: 0.7660 (tp30) REVERT: A 1155 ASN cc_start: 0.8702 (m-40) cc_final: 0.7604 (t0) REVERT: A 1260 TYR cc_start: 0.7629 (m-10) cc_final: 0.7306 (m-10) REVERT: B 198 PHE cc_start: 0.8669 (m-10) cc_final: 0.8451 (m-10) REVERT: B 247 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7134 (mtt90) REVERT: B 286 ASP cc_start: 0.8756 (t70) cc_final: 0.8387 (t0) REVERT: B 293 PHE cc_start: 0.8880 (t80) cc_final: 0.8570 (t80) REVERT: B 372 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8782 (tt0) REVERT: B 382 THR cc_start: 0.8162 (m) cc_final: 0.7877 (t) REVERT: B 633 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8045 (mm-40) REVERT: B 641 GLU cc_start: 0.8377 (tp30) cc_final: 0.8129 (tp30) REVERT: B 664 TRP cc_start: 0.6897 (m-10) cc_final: 0.6409 (m100) REVERT: B 701 GLU cc_start: 0.8216 (pt0) cc_final: 0.7777 (pm20) REVERT: B 702 CYS cc_start: 0.8061 (m) cc_final: 0.7712 (m) REVERT: B 775 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: B 803 MET cc_start: 0.8917 (mmm) cc_final: 0.8701 (mmp) REVERT: B 822 SER cc_start: 0.8695 (m) cc_final: 0.8423 (t) REVERT: B 824 ILE cc_start: 0.8739 (mm) cc_final: 0.8428 (tp) REVERT: B 829 PHE cc_start: 0.7391 (m-80) cc_final: 0.6911 (p90) REVERT: B 898 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7339 (tpp80) REVERT: B 928 MET cc_start: 0.8421 (tpp) cc_final: 0.7892 (tpp) REVERT: B 973 ARG cc_start: 0.7013 (mtt180) cc_final: 0.6715 (mtp85) REVERT: B 982 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: B 1059 MET cc_start: 0.8525 (ttm) cc_final: 0.8191 (ttm) REVERT: B 1066 ASN cc_start: 0.8917 (m110) cc_final: 0.8553 (m110) REVERT: B 1076 GLN cc_start: 0.7939 (mp10) cc_final: 0.7104 (tp-100) REVERT: B 1152 GLU cc_start: 0.8361 (tp30) cc_final: 0.7750 (tp30) REVERT: B 1155 ASN cc_start: 0.8741 (m-40) cc_final: 0.7891 (t0) REVERT: B 1161 GLU cc_start: 0.7350 (pm20) cc_final: 0.7002 (pm20) REVERT: C 286 ASP cc_start: 0.8676 (t70) cc_final: 0.8278 (t70) REVERT: C 382 THR cc_start: 0.8020 (m) cc_final: 0.7775 (t) REVERT: C 663 LYS cc_start: 0.8783 (tttt) cc_final: 0.8550 (tppp) REVERT: C 664 TRP cc_start: 0.6849 (m-10) cc_final: 0.6342 (m100) REVERT: C 680 MET cc_start: 0.8055 (mmt) cc_final: 0.7512 (mtp) REVERT: C 701 GLU cc_start: 0.8285 (pt0) cc_final: 0.7833 (pm20) REVERT: C 702 CYS cc_start: 0.7833 (m) cc_final: 0.7454 (m) REVERT: C 711 GLN cc_start: 0.8820 (tt0) cc_final: 0.8212 (mt0) REVERT: C 805 GLN cc_start: 0.8613 (mt0) cc_final: 0.8122 (mp10) REVERT: C 829 PHE cc_start: 0.7417 (m-80) cc_final: 0.6833 (p90) REVERT: C 883 LYS cc_start: 0.9115 (mttm) cc_final: 0.8840 (mmtp) REVERT: C 898 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7401 (tpp80) REVERT: C 925 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8415 (tt0) REVERT: C 928 MET cc_start: 0.8485 (tpp) cc_final: 0.7761 (tpp) REVERT: C 938 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8095 (tpm-80) REVERT: C 973 ARG cc_start: 0.6952 (mtt180) cc_final: 0.6690 (mtp85) REVERT: C 1075 LEU cc_start: 0.8613 (mm) cc_final: 0.8300 (mm) REVERT: C 1076 GLN cc_start: 0.7846 (mp10) cc_final: 0.6945 (tp40) REVERT: C 1141 LYS cc_start: 0.8754 (mttt) cc_final: 0.8309 (mtpt) REVERT: C 1152 GLU cc_start: 0.8289 (tp30) cc_final: 0.7544 (tp30) REVERT: C 1155 ASN cc_start: 0.8803 (m-40) cc_final: 0.7919 (t0) REVERT: C 1331 MET cc_start: 0.6550 (mpp) cc_final: 0.6185 (tpt) outliers start: 153 outliers final: 101 residues processed: 702 average time/residue: 0.1888 time to fit residues: 225.0492 Evaluate side-chains 656 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 549 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 476 TRP Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 668 PHE Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 170 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 272 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 346 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 515 HIS A 844 HIS A1269 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS B1269 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 623 GLN C 844 HIS C1269 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.171188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.126963 restraints weight = 52327.121| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 4.02 r_work: 0.3462 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33048 Z= 0.130 Angle : 0.774 14.012 45426 Z= 0.354 Chirality : 0.048 0.341 5778 Planarity : 0.003 0.046 5376 Dihedral : 5.933 30.010 4014 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 3.48 % Allowed : 19.13 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.83 (0.13), residues: 3717 helix: 0.64 (0.20), residues: 747 sheet: -1.85 (0.17), residues: 888 loop : -2.99 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 977 TYR 0.029 0.001 TYR C1067 PHE 0.034 0.001 PHE B 104 TRP 0.029 0.001 TRP B 222 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (32790) covalent geometry : angle 0.68550 / 0.33 (44703) SS BOND : bond 0.00445 / 0.29 ( 42) SS BOND : angle 2.01143 / 1.55 ( 84) hydrogen bonds : bond 0.03663 / 2.57 ( 851) hydrogen bonds : angle 5.13015 / 3.53 ( 2427) Misc. bond : bond 0.00091 / 0.05 ( 3) link_ALPHA1-2 : bond 0.00879 / 0.44 ( 6) link_ALPHA1-2 : angle 1.88686 / 0.99 ( 18) link_ALPHA1-3 : bond 0.00610 / 0.28 ( 12) link_ALPHA1-3 : angle 3.39106 / 2.14 ( 36) link_ALPHA1-6 : bond 0.01047 / 0.69 ( 24) link_ALPHA1-6 : angle 1.83197 / 1.25 ( 72) link_BETA1-4 : bond 0.00979 / 0.68 ( 87) link_BETA1-4 : angle 2.57100 / 1.78 ( 261) link_BETA1-6 : bond 0.00381 / 0.19 ( 3) link_BETA1-6 : angle 1.21598 / 0.76 ( 9) link_NAG-ASN : bond 0.00638 / 0.43 ( 81) link_NAG-ASN : angle 3.75361 / 2.37 ( 243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 579 time to evaluate : 1.147 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: A 215 LYS cc_start: 0.8504 (mttt) cc_final: 0.8203 (mttt) REVERT: A 245 VAL cc_start: 0.8518 (t) cc_final: 0.8170 (t) REVERT: A 247 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7539 (mtm110) REVERT: A 286 ASP cc_start: 0.8474 (t70) cc_final: 0.8251 (t0) REVERT: A 371 ASP cc_start: 0.7139 (p0) cc_final: 0.6396 (m-30) REVERT: A 372 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: A 382 THR cc_start: 0.7909 (m) cc_final: 0.7614 (t) REVERT: A 461 LYS cc_start: 0.8903 (tttt) cc_final: 0.8614 (tttm) REVERT: A 597 GLN cc_start: 0.8502 (mt0) cc_final: 0.8212 (tt0) REVERT: A 641 GLU cc_start: 0.8435 (tp30) cc_final: 0.8186 (tp30) REVERT: A 663 LYS cc_start: 0.8770 (tptp) cc_final: 0.8295 (tptt) REVERT: A 664 TRP cc_start: 0.6806 (m-10) cc_final: 0.6258 (m100) REVERT: A 680 MET cc_start: 0.8282 (mmt) cc_final: 0.7782 (mtp) REVERT: A 702 CYS cc_start: 0.7803 (m) cc_final: 0.7550 (m) REVERT: A 824 ILE cc_start: 0.8816 (mm) cc_final: 0.8502 (tp) REVERT: A 829 PHE cc_start: 0.7393 (m-80) cc_final: 0.6987 (p90) REVERT: A 898 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7590 (tpp80) REVERT: A 928 MET cc_start: 0.8596 (tpp) cc_final: 0.8132 (tpp) REVERT: A 973 ARG cc_start: 0.6903 (mtt180) cc_final: 0.6603 (mtp85) REVERT: A 1059 MET cc_start: 0.8734 (ttm) cc_final: 0.8494 (ttm) REVERT: A 1076 GLN cc_start: 0.8000 (mp10) cc_final: 0.7060 (tp40) REVERT: A 1141 LYS cc_start: 0.8845 (mttt) cc_final: 0.8432 (mtpt) REVERT: A 1152 GLU cc_start: 0.8326 (tp30) cc_final: 0.7661 (tp30) REVERT: A 1155 ASN cc_start: 0.8746 (m-40) cc_final: 0.7948 (t0) REVERT: A 1161 GLU cc_start: 0.7500 (pm20) cc_final: 0.7119 (pm20) REVERT: A 1260 TYR cc_start: 0.7807 (m-10) cc_final: 0.7509 (m-10) REVERT: A 1279 MET cc_start: 0.8262 (mmt) cc_final: 0.8037 (mmt) REVERT: A 1331 MET cc_start: 0.6790 (ttt) cc_final: 0.6301 (tmm) REVERT: B 247 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7243 (mtt90) REVERT: B 286 ASP cc_start: 0.8681 (t70) cc_final: 0.8335 (t0) REVERT: B 293 PHE cc_start: 0.8747 (t80) cc_final: 0.8544 (t80) REVERT: B 372 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8756 (tt0) REVERT: B 382 THR cc_start: 0.8011 (m) cc_final: 0.7744 (t) REVERT: B 603 LEU cc_start: 0.9094 (tp) cc_final: 0.8757 (tp) REVERT: B 633 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8093 (mm-40) REVERT: B 664 TRP cc_start: 0.6890 (m-10) cc_final: 0.6586 (m100) REVERT: B 680 MET cc_start: 0.8559 (mmm) cc_final: 0.8007 (mtp) REVERT: B 701 GLU cc_start: 0.8205 (pt0) cc_final: 0.7781 (pm20) REVERT: B 702 CYS cc_start: 0.7880 (m) cc_final: 0.7545 (m) REVERT: B 775 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: B 822 SER cc_start: 0.8811 (m) cc_final: 0.8577 (t) REVERT: B 824 ILE cc_start: 0.8780 (mm) cc_final: 0.8488 (tp) REVERT: B 829 PHE cc_start: 0.7366 (m-80) cc_final: 0.7006 (p90) REVERT: B 898 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7526 (tpp80) REVERT: B 925 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8233 (tt0) REVERT: B 973 ARG cc_start: 0.7045 (mtt180) cc_final: 0.6725 (mtp85) REVERT: B 1059 MET cc_start: 0.8585 (ttm) cc_final: 0.8301 (ttm) REVERT: B 1066 ASN cc_start: 0.8786 (m110) cc_final: 0.8453 (m110) REVERT: B 1120 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8318 (mttt) REVERT: B 1152 GLU cc_start: 0.8337 (tp30) cc_final: 0.7760 (tp30) REVERT: B 1155 ASN cc_start: 0.8753 (m-40) cc_final: 0.8059 (t0) REVERT: B 1161 GLU cc_start: 0.7417 (pm20) cc_final: 0.7141 (pm20) REVERT: B 1263 LEU cc_start: 0.9016 (tp) cc_final: 0.8812 (tt) REVERT: B 1283 ARG cc_start: 0.9003 (mtt90) cc_final: 0.8144 (mtm180) REVERT: C 140 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7369 (tm-30) REVERT: C 286 ASP cc_start: 0.8597 (t70) cc_final: 0.8093 (t70) REVERT: C 293 PHE cc_start: 0.8697 (t80) cc_final: 0.8078 (t80) REVERT: C 382 THR cc_start: 0.7905 (m) cc_final: 0.7682 (t) REVERT: C 570 GLU cc_start: 0.7464 (mp0) cc_final: 0.7237 (mp0) REVERT: C 663 LYS cc_start: 0.8818 (tttt) cc_final: 0.8597 (tppp) REVERT: C 664 TRP cc_start: 0.6956 (m-10) cc_final: 0.6464 (m100) REVERT: C 680 MET cc_start: 0.8151 (mmt) cc_final: 0.7659 (mtp) REVERT: C 701 GLU cc_start: 0.8293 (pt0) cc_final: 0.7925 (pm20) REVERT: C 711 GLN cc_start: 0.8764 (tt0) cc_final: 0.8222 (mt0) REVERT: C 805 GLN cc_start: 0.8643 (mt0) cc_final: 0.8223 (mp10) REVERT: C 829 PHE cc_start: 0.7398 (m-80) cc_final: 0.6989 (p90) REVERT: C 883 LYS cc_start: 0.9107 (mttm) cc_final: 0.8880 (mmtp) REVERT: C 898 ARG cc_start: 0.8320 (ttp80) cc_final: 0.7504 (tpp80) REVERT: C 925 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8137 (tt0) REVERT: C 928 MET cc_start: 0.8663 (tpp) cc_final: 0.8035 (tpp) REVERT: C 938 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8187 (tpm-80) REVERT: C 973 ARG cc_start: 0.6958 (mtt180) cc_final: 0.6695 (mtp85) REVERT: C 1075 LEU cc_start: 0.8663 (mm) cc_final: 0.8386 (mm) REVERT: C 1076 GLN cc_start: 0.7972 (mp10) cc_final: 0.7128 (tp40) REVERT: C 1141 LYS cc_start: 0.8796 (mttt) cc_final: 0.8393 (mtpt) REVERT: C 1152 GLU cc_start: 0.8360 (tp30) cc_final: 0.7653 (tp30) REVERT: C 1155 ASN cc_start: 0.8839 (m-40) cc_final: 0.8150 (t0) outliers start: 114 outliers final: 74 residues processed: 659 average time/residue: 0.1877 time to fit residues: 209.0427 Evaluate side-chains 638 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 559 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1317 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 329 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 352 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 351 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS A 321 GLN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B1298 GLN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.169549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125099 restraints weight = 51960.694| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.97 r_work: 0.3435 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33048 Z= 0.165 Angle : 0.781 13.763 45426 Z= 0.358 Chirality : 0.048 0.338 5778 Planarity : 0.003 0.046 5376 Dihedral : 5.898 30.052 4014 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 4.09 % Allowed : 20.04 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.72 (0.13), residues: 3717 helix: 0.81 (0.20), residues: 747 sheet: -1.81 (0.17), residues: 879 loop : -2.94 (0.12), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1212 TYR 0.022 0.001 TYR B 204 PHE 0.029 0.001 PHE B 104 TRP 0.023 0.001 TRP C 222 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (32790) covalent geometry : angle 0.69538 / 0.34 (44703) SS BOND : bond 0.00728 / 0.48 ( 42) SS BOND : angle 1.62321 / 1.24 ( 84) hydrogen bonds : bond 0.03789 / 2.65 ( 851) hydrogen bonds : angle 5.09146 / 3.52 ( 2427) Misc. bond : bond 0.00112 / 0.06 ( 3) link_ALPHA1-2 : bond 0.00914 / 0.45 ( 6) link_ALPHA1-2 : angle 1.60660 / 0.90 ( 18) link_ALPHA1-3 : bond 0.00598 / 0.28 ( 12) link_ALPHA1-3 : angle 3.29703 / 2.09 ( 36) link_ALPHA1-6 : bond 0.00930 / 0.61 ( 24) link_ALPHA1-6 : angle 1.79889 / 1.23 ( 72) link_BETA1-4 : bond 0.00924 / 0.65 ( 87) link_BETA1-4 : angle 2.58110 / 1.78 ( 261) link_BETA1-6 : bond 0.00342 / 0.17 ( 3) link_BETA1-6 : angle 1.23995 / 0.78 ( 9) link_NAG-ASN : bond 0.00580 / 0.39 ( 81) link_NAG-ASN : angle 3.76354 / 2.38 ( 243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 564 time to evaluate : 1.175 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: A 215 LYS cc_start: 0.8576 (mttt) cc_final: 0.8245 (mttt) REVERT: A 286 ASP cc_start: 0.8544 (t70) cc_final: 0.8262 (t0) REVERT: A 371 ASP cc_start: 0.7212 (p0) cc_final: 0.6408 (m-30) REVERT: A 372 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8621 (tt0) REVERT: A 382 THR cc_start: 0.7899 (m) cc_final: 0.7667 (t) REVERT: A 461 LYS cc_start: 0.8945 (tttt) cc_final: 0.8504 (tmtt) REVERT: A 477 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7667 (p) REVERT: A 597 GLN cc_start: 0.8525 (mt0) cc_final: 0.8231 (tt0) REVERT: A 641 GLU cc_start: 0.8458 (tp30) cc_final: 0.8134 (tp30) REVERT: A 663 LYS cc_start: 0.8849 (tptp) cc_final: 0.8336 (tptt) REVERT: A 680 MET cc_start: 0.8299 (mmt) cc_final: 0.7767 (mtp) REVERT: A 702 CYS cc_start: 0.7845 (m) cc_final: 0.7575 (m) REVERT: A 824 ILE cc_start: 0.8821 (mm) cc_final: 0.8513 (tp) REVERT: A 829 PHE cc_start: 0.7441 (m-80) cc_final: 0.6974 (p90) REVERT: A 833 ASN cc_start: 0.9039 (t0) cc_final: 0.8809 (t0) REVERT: A 898 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7602 (tpp80) REVERT: A 928 MET cc_start: 0.8616 (tpp) cc_final: 0.8101 (tpp) REVERT: A 973 ARG cc_start: 0.6875 (mtt180) cc_final: 0.6597 (mtp85) REVERT: A 1023 VAL cc_start: 0.9460 (OUTLIER) cc_final: 0.8981 (m) REVERT: A 1059 MET cc_start: 0.8765 (ttm) cc_final: 0.8546 (ttm) REVERT: A 1141 LYS cc_start: 0.8887 (mttt) cc_final: 0.8454 (mtpt) REVERT: A 1152 GLU cc_start: 0.8427 (tp30) cc_final: 0.7797 (tp30) REVERT: A 1155 ASN cc_start: 0.8806 (m-40) cc_final: 0.7905 (t0) REVERT: A 1260 TYR cc_start: 0.7823 (m-10) cc_final: 0.7485 (m-10) REVERT: A 1279 MET cc_start: 0.8248 (mmt) cc_final: 0.8029 (mmt) REVERT: A 1331 MET cc_start: 0.6805 (ttt) cc_final: 0.6292 (tmm) REVERT: B 286 ASP cc_start: 0.8726 (t70) cc_final: 0.8366 (t0) REVERT: B 364 TYR cc_start: 0.8069 (m-80) cc_final: 0.7826 (m-80) REVERT: B 372 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8759 (tt0) REVERT: B 382 THR cc_start: 0.8100 (m) cc_final: 0.7815 (t) REVERT: B 560 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8660 (mppt) REVERT: B 603 LEU cc_start: 0.9106 (tp) cc_final: 0.8746 (tp) REVERT: B 623 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: B 633 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8124 (mm-40) REVERT: B 664 TRP cc_start: 0.6915 (m-10) cc_final: 0.6563 (m100) REVERT: B 680 MET cc_start: 0.8569 (mmm) cc_final: 0.8044 (mtp) REVERT: B 702 CYS cc_start: 0.7864 (m) cc_final: 0.7462 (m) REVERT: B 775 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7926 (pm20) REVERT: B 822 SER cc_start: 0.8835 (m) cc_final: 0.8593 (t) REVERT: B 824 ILE cc_start: 0.8774 (mm) cc_final: 0.8488 (tp) REVERT: B 829 PHE cc_start: 0.7319 (m-80) cc_final: 0.7034 (p90) REVERT: B 925 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8330 (tt0) REVERT: B 973 ARG cc_start: 0.7041 (mtt180) cc_final: 0.6757 (mtp85) REVERT: B 1059 MET cc_start: 0.8625 (ttm) cc_final: 0.8344 (ttm) REVERT: B 1066 ASN cc_start: 0.8874 (m110) cc_final: 0.8534 (m110) REVERT: B 1120 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8316 (mttt) REVERT: B 1152 GLU cc_start: 0.8345 (tp30) cc_final: 0.7772 (tp30) REVERT: B 1155 ASN cc_start: 0.8752 (m-40) cc_final: 0.8114 (t0) REVERT: B 1161 GLU cc_start: 0.7424 (pm20) cc_final: 0.7120 (pm20) REVERT: C 286 ASP cc_start: 0.8617 (t70) cc_final: 0.8216 (t0) REVERT: C 293 PHE cc_start: 0.8695 (t80) cc_final: 0.8125 (t80) REVERT: C 382 THR cc_start: 0.7976 (m) cc_final: 0.7760 (t) REVERT: C 570 GLU cc_start: 0.7499 (mp0) cc_final: 0.7294 (mp0) REVERT: C 641 GLU cc_start: 0.8469 (tp30) cc_final: 0.7801 (tp30) REVERT: C 663 LYS cc_start: 0.8835 (tttt) cc_final: 0.8602 (tppp) REVERT: C 664 TRP cc_start: 0.7009 (m-10) cc_final: 0.6516 (m100) REVERT: C 680 MET cc_start: 0.8169 (mmt) cc_final: 0.7607 (mtp) REVERT: C 701 GLU cc_start: 0.8086 (pt0) cc_final: 0.7743 (pm20) REVERT: C 711 GLN cc_start: 0.8806 (tt0) cc_final: 0.8280 (mt0) REVERT: C 805 GLN cc_start: 0.8678 (mt0) cc_final: 0.8274 (mp10) REVERT: C 829 PHE cc_start: 0.7420 (m-80) cc_final: 0.6966 (p90) REVERT: C 833 ASN cc_start: 0.9124 (t0) cc_final: 0.8852 (t0) REVERT: C 883 LYS cc_start: 0.9130 (mttm) cc_final: 0.8886 (mmtp) REVERT: C 898 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7535 (tpp80) REVERT: C 925 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8201 (tt0) REVERT: C 928 MET cc_start: 0.8734 (tpp) cc_final: 0.8210 (tpp) REVERT: C 938 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8244 (tpm-80) REVERT: C 973 ARG cc_start: 0.6980 (mtt180) cc_final: 0.6725 (mtp85) REVERT: C 1141 LYS cc_start: 0.8804 (mttt) cc_final: 0.8374 (mtpt) REVERT: C 1152 GLU cc_start: 0.8361 (tp30) cc_final: 0.7681 (tp30) REVERT: C 1155 ASN cc_start: 0.8860 (m-40) cc_final: 0.8181 (t0) outliers start: 134 outliers final: 102 residues processed: 648 average time/residue: 0.1887 time to fit residues: 207.2700 Evaluate side-chains 653 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 544 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 623 GLN Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1317 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 66 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 154 optimal weight: 0.1980 chunk 185 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.165957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.125194 restraints weight = 51568.423| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.77 r_work: 0.3436 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 33048 Z= 0.183 Angle : 0.794 13.848 45426 Z= 0.366 Chirality : 0.049 0.343 5778 Planarity : 0.003 0.047 5376 Dihedral : 5.916 29.887 4014 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 4.28 % Allowed : 20.16 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.13), residues: 3717 helix: 0.89 (0.20), residues: 753 sheet: -1.79 (0.17), residues: 891 loop : -2.86 (0.12), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 898 TYR 0.032 0.001 TYR C1067 PHE 0.036 0.001 PHE B 293 TRP 0.035 0.002 TRP B 222 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (32790) covalent geometry : angle 0.71089 / 0.35 (44703) SS BOND : bond 0.00826 / 0.61 ( 42) SS BOND : angle 1.66731 / 1.24 ( 84) hydrogen bonds : bond 0.03884 / 2.73 ( 851) hydrogen bonds : angle 5.10573 / 3.54 ( 2427) Misc. bond : bond 0.00111 / 0.06 ( 3) link_ALPHA1-2 : bond 0.00890 / 0.44 ( 6) link_ALPHA1-2 : angle 1.58656 / 0.89 ( 18) link_ALPHA1-3 : bond 0.00576 / 0.27 ( 12) link_ALPHA1-3 : angle 3.25469 / 2.06 ( 36) link_ALPHA1-6 : bond 0.00843 / 0.56 ( 24) link_ALPHA1-6 : angle 1.71720 / 1.18 ( 72) link_BETA1-4 : bond 0.00942 / 0.66 ( 87) link_BETA1-4 : angle 2.53693 / 1.75 ( 261) link_BETA1-6 : bond 0.00317 / 0.16 ( 3) link_BETA1-6 : angle 1.27445 / 0.79 ( 9) link_NAG-ASN : bond 0.00569 / 0.38 ( 81) link_NAG-ASN : angle 3.80264 / 2.40 ( 243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 554 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: A 215 LYS cc_start: 0.8558 (mttt) cc_final: 0.8270 (mttt) REVERT: A 286 ASP cc_start: 0.8594 (t70) cc_final: 0.8283 (t0) REVERT: A 371 ASP cc_start: 0.7215 (p0) cc_final: 0.6435 (m-30) REVERT: A 372 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: A 382 THR cc_start: 0.7945 (m) cc_final: 0.7649 (t) REVERT: A 461 LYS cc_start: 0.8965 (tttt) cc_final: 0.8537 (tmtt) REVERT: A 477 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7773 (p) REVERT: A 664 TRP cc_start: 0.6801 (m-10) cc_final: 0.6444 (m100) REVERT: A 702 CYS cc_start: 0.7750 (m) cc_final: 0.7440 (m) REVERT: A 824 ILE cc_start: 0.8846 (mm) cc_final: 0.8561 (tp) REVERT: A 829 PHE cc_start: 0.7535 (m-80) cc_final: 0.7043 (p90) REVERT: A 833 ASN cc_start: 0.9031 (t0) cc_final: 0.8805 (t0) REVERT: A 898 ARG cc_start: 0.8361 (ttp80) cc_final: 0.7618 (tpp80) REVERT: A 923 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8505 (ttp80) REVERT: A 925 GLU cc_start: 0.8909 (tt0) cc_final: 0.8317 (tt0) REVERT: A 928 MET cc_start: 0.8626 (tpp) cc_final: 0.8098 (tpp) REVERT: A 1023 VAL cc_start: 0.9487 (OUTLIER) cc_final: 0.9036 (m) REVERT: A 1059 MET cc_start: 0.8752 (ttm) cc_final: 0.8518 (ttm) REVERT: A 1141 LYS cc_start: 0.8887 (mttt) cc_final: 0.8420 (mtpt) REVERT: A 1152 GLU cc_start: 0.8425 (tp30) cc_final: 0.7748 (tp30) REVERT: A 1155 ASN cc_start: 0.8812 (m-40) cc_final: 0.8098 (t0) REVERT: A 1260 TYR cc_start: 0.7789 (m-10) cc_final: 0.7473 (m-10) REVERT: B 286 ASP cc_start: 0.8737 (t70) cc_final: 0.8364 (t0) REVERT: B 364 TYR cc_start: 0.8038 (m-80) cc_final: 0.7783 (m-80) REVERT: B 372 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8703 (tt0) REVERT: B 382 THR cc_start: 0.8148 (m) cc_final: 0.7830 (t) REVERT: B 633 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8164 (mm-40) REVERT: B 664 TRP cc_start: 0.6884 (m-10) cc_final: 0.6497 (m100) REVERT: B 680 MET cc_start: 0.8537 (mmm) cc_final: 0.8088 (mtp) REVERT: B 702 CYS cc_start: 0.7800 (m) cc_final: 0.7392 (m) REVERT: B 775 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: B 822 SER cc_start: 0.8847 (m) cc_final: 0.8607 (t) REVERT: B 824 ILE cc_start: 0.8781 (mm) cc_final: 0.8493 (tp) REVERT: B 829 PHE cc_start: 0.7395 (m-80) cc_final: 0.7036 (p90) REVERT: B 898 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7589 (tpp80) REVERT: B 925 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8364 (tt0) REVERT: B 973 ARG cc_start: 0.6996 (mtt180) cc_final: 0.6729 (mtp85) REVERT: B 1023 VAL cc_start: 0.9288 (t) cc_final: 0.8896 (m) REVERT: B 1059 MET cc_start: 0.8609 (ttm) cc_final: 0.8320 (ttm) REVERT: B 1066 ASN cc_start: 0.8890 (m110) cc_final: 0.8567 (m110) REVERT: B 1120 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8347 (mttt) REVERT: B 1152 GLU cc_start: 0.8308 (tp30) cc_final: 0.7765 (tp30) REVERT: B 1155 ASN cc_start: 0.8746 (m-40) cc_final: 0.8099 (t0) REVERT: B 1161 GLU cc_start: 0.7470 (pm20) cc_final: 0.7142 (pm20) REVERT: C 286 ASP cc_start: 0.8702 (t70) cc_final: 0.8406 (t0) REVERT: C 293 PHE cc_start: 0.8685 (t80) cc_final: 0.8172 (t80) REVERT: C 371 ASP cc_start: 0.7035 (p0) cc_final: 0.6596 (m-30) REVERT: C 382 THR cc_start: 0.7998 (m) cc_final: 0.7764 (t) REVERT: C 570 GLU cc_start: 0.7495 (mp0) cc_final: 0.7290 (mp0) REVERT: C 663 LYS cc_start: 0.8880 (tttt) cc_final: 0.8616 (tppp) REVERT: C 664 TRP cc_start: 0.7053 (m-10) cc_final: 0.6508 (m100) REVERT: C 680 MET cc_start: 0.8163 (mmt) cc_final: 0.7604 (mtp) REVERT: C 694 ILE cc_start: 0.5299 (OUTLIER) cc_final: 0.4665 (tp) REVERT: C 711 GLN cc_start: 0.8777 (tt0) cc_final: 0.8248 (mt0) REVERT: C 775 GLN cc_start: 0.8550 (pt0) cc_final: 0.8131 (pm20) REVERT: C 805 GLN cc_start: 0.8664 (mt0) cc_final: 0.8267 (mp10) REVERT: C 829 PHE cc_start: 0.7460 (m-80) cc_final: 0.6972 (p90) REVERT: C 850 ASP cc_start: 0.8445 (t0) cc_final: 0.8148 (t0) REVERT: C 883 LYS cc_start: 0.9117 (mttm) cc_final: 0.8861 (mmtp) REVERT: C 898 ARG cc_start: 0.8360 (ttp80) cc_final: 0.7559 (tpp80) REVERT: C 925 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8289 (tt0) REVERT: C 928 MET cc_start: 0.8743 (tpp) cc_final: 0.8152 (tpp) REVERT: C 938 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8252 (tpm-80) REVERT: C 973 ARG cc_start: 0.6981 (mtt180) cc_final: 0.6685 (mtp85) REVERT: C 1023 VAL cc_start: 0.9392 (t) cc_final: 0.9134 (m) REVERT: C 1075 LEU cc_start: 0.8515 (mm) cc_final: 0.8199 (mm) REVERT: C 1076 GLN cc_start: 0.7947 (mp10) cc_final: 0.7074 (tp40) REVERT: C 1141 LYS cc_start: 0.8806 (mttt) cc_final: 0.8361 (mtpt) REVERT: C 1152 GLU cc_start: 0.8396 (tp30) cc_final: 0.7715 (tp30) REVERT: C 1155 ASN cc_start: 0.8878 (m-40) cc_final: 0.8156 (t0) REVERT: C 1331 MET cc_start: 0.7177 (tpp) cc_final: 0.6314 (tpt) outliers start: 140 outliers final: 112 residues processed: 645 average time/residue: 0.1892 time to fit residues: 206.4077 Evaluate side-chains 651 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 532 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1293 MET Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1318 VAL Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 668 PHE Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 369 optimal weight: 0.0670 chunk 202 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 322 optimal weight: 0.7980 chunk 354 optimal weight: 0.0980 chunk 311 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 293 optimal weight: 0.8980 chunk 316 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1088 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.172012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.127914 restraints weight = 52323.827| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.06 r_work: 0.3472 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33048 Z= 0.119 Angle : 0.752 13.878 45426 Z= 0.347 Chirality : 0.047 0.334 5778 Planarity : 0.003 0.046 5376 Dihedral : 5.695 29.174 4014 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.24 % Allowed : 21.72 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.14), residues: 3717 helix: 1.13 (0.20), residues: 747 sheet: -1.54 (0.18), residues: 879 loop : -2.82 (0.12), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 977 TYR 0.018 0.001 TYR B 204 PHE 0.035 0.001 PHE B 293 TRP 0.031 0.002 TRP A 222 HIS 0.005 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (32790) covalent geometry : angle 0.67160 / 0.33 (44703) SS BOND : bond 0.00464 / 0.31 ( 42) SS BOND : angle 1.94465 / 1.33 ( 84) hydrogen bonds : bond 0.03322 / 2.34 ( 851) hydrogen bonds : angle 4.91773 / 3.40 ( 2427) Misc. bond : bond 0.00052 / 0.03 ( 3) link_ALPHA1-2 : bond 0.00837 / 0.42 ( 6) link_ALPHA1-2 : angle 1.53829 / 0.86 ( 18) link_ALPHA1-3 : bond 0.00570 / 0.26 ( 12) link_ALPHA1-3 : angle 3.12446 / 1.98 ( 36) link_ALPHA1-6 : bond 0.00848 / 0.56 ( 24) link_ALPHA1-6 : angle 1.54325 / 1.07 ( 72) link_BETA1-4 : bond 0.00915 / 0.64 ( 87) link_BETA1-4 : angle 2.39449 / 1.64 ( 261) link_BETA1-6 : bond 0.00422 / 0.21 ( 3) link_BETA1-6 : angle 1.20092 / 0.75 ( 9) link_NAG-ASN : bond 0.00622 / 0.41 ( 81) link_NAG-ASN : angle 3.60676 / 2.27 ( 243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 583 time to evaluate : 1.194 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: A 286 ASP cc_start: 0.8620 (t70) cc_final: 0.8275 (t0) REVERT: A 293 PHE cc_start: 0.8641 (t80) cc_final: 0.7738 (t80) REVERT: A 371 ASP cc_start: 0.7051 (p0) cc_final: 0.6273 (m-30) REVERT: A 372 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: A 382 THR cc_start: 0.7932 (m) cc_final: 0.7598 (t) REVERT: A 461 LYS cc_start: 0.8931 (tttt) cc_final: 0.8595 (tttt) REVERT: A 664 TRP cc_start: 0.6720 (m-10) cc_final: 0.6229 (m100) REVERT: A 680 MET cc_start: 0.8037 (mmt) cc_final: 0.7384 (mtp) REVERT: A 702 CYS cc_start: 0.7732 (m) cc_final: 0.7486 (m) REVERT: A 824 ILE cc_start: 0.8789 (mm) cc_final: 0.8501 (tp) REVERT: A 829 PHE cc_start: 0.7475 (m-80) cc_final: 0.7085 (p90) REVERT: A 833 ASN cc_start: 0.9032 (t0) cc_final: 0.8814 (t0) REVERT: A 898 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7500 (tpp80) REVERT: A 923 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8475 (ttp80) REVERT: A 925 GLU cc_start: 0.8910 (tt0) cc_final: 0.8358 (tt0) REVERT: A 928 MET cc_start: 0.8618 (tpp) cc_final: 0.8065 (tpp) REVERT: A 1023 VAL cc_start: 0.9447 (t) cc_final: 0.8983 (m) REVERT: A 1059 MET cc_start: 0.8725 (ttm) cc_final: 0.8489 (ttm) REVERT: A 1141 LYS cc_start: 0.8834 (mttt) cc_final: 0.8382 (mtpt) REVERT: A 1152 GLU cc_start: 0.8412 (tp30) cc_final: 0.7757 (tp30) REVERT: A 1155 ASN cc_start: 0.8766 (m-40) cc_final: 0.7896 (t0) REVERT: A 1260 TYR cc_start: 0.7793 (m-10) cc_final: 0.7509 (m-10) REVERT: B 286 ASP cc_start: 0.8691 (t70) cc_final: 0.8145 (t0) REVERT: B 364 TYR cc_start: 0.7970 (m-80) cc_final: 0.7761 (m-80) REVERT: B 371 ASP cc_start: 0.6989 (p0) cc_final: 0.6361 (m-30) REVERT: B 372 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: B 382 THR cc_start: 0.8034 (m) cc_final: 0.7721 (t) REVERT: B 583 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7812 (mm-40) REVERT: B 633 GLN cc_start: 0.8509 (mm-40) cc_final: 0.7960 (mm-40) REVERT: B 657 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8159 (p) REVERT: B 664 TRP cc_start: 0.6875 (m-10) cc_final: 0.6475 (m100) REVERT: B 680 MET cc_start: 0.8459 (mmm) cc_final: 0.7996 (mtp) REVERT: B 702 CYS cc_start: 0.7750 (m) cc_final: 0.7379 (m) REVERT: B 775 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: B 805 GLN cc_start: 0.8698 (mt0) cc_final: 0.8395 (mp10) REVERT: B 822 SER cc_start: 0.8871 (m) cc_final: 0.8606 (t) REVERT: B 824 ILE cc_start: 0.8728 (mm) cc_final: 0.8458 (tp) REVERT: B 829 PHE cc_start: 0.7339 (m-80) cc_final: 0.7040 (p90) REVERT: B 925 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8321 (tt0) REVERT: B 973 ARG cc_start: 0.6990 (mtt180) cc_final: 0.6730 (mtp85) REVERT: B 1059 MET cc_start: 0.8594 (ttm) cc_final: 0.8317 (ttm) REVERT: B 1066 ASN cc_start: 0.8782 (m110) cc_final: 0.8473 (m110) REVERT: B 1120 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8341 (mttt) REVERT: B 1152 GLU cc_start: 0.8304 (tp30) cc_final: 0.7729 (tp30) REVERT: B 1155 ASN cc_start: 0.8711 (m-40) cc_final: 0.8083 (t0) REVERT: B 1161 GLU cc_start: 0.7486 (pm20) cc_final: 0.7210 (pm20) REVERT: B 1199 MET cc_start: 0.8258 (mtt) cc_final: 0.7905 (mtp) REVERT: C 93 ASN cc_start: 0.8251 (t0) cc_final: 0.7376 (t0) REVERT: C 247 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7500 (mtt90) REVERT: C 286 ASP cc_start: 0.8666 (t70) cc_final: 0.8405 (t0) REVERT: C 293 PHE cc_start: 0.8645 (t80) cc_final: 0.8004 (t80) REVERT: C 371 ASP cc_start: 0.6903 (p0) cc_final: 0.6518 (m-30) REVERT: C 382 THR cc_start: 0.7857 (m) cc_final: 0.7621 (t) REVERT: C 444 ASP cc_start: 0.8463 (p0) cc_final: 0.8261 (p0) REVERT: C 641 GLU cc_start: 0.8398 (tp30) cc_final: 0.7718 (tp30) REVERT: C 663 LYS cc_start: 0.8813 (tttt) cc_final: 0.8580 (tppp) REVERT: C 664 TRP cc_start: 0.6969 (m-10) cc_final: 0.6451 (m100) REVERT: C 680 MET cc_start: 0.8152 (mmt) cc_final: 0.7603 (mtp) REVERT: C 711 GLN cc_start: 0.8748 (tt0) cc_final: 0.8237 (mt0) REVERT: C 805 GLN cc_start: 0.8675 (mt0) cc_final: 0.8312 (mp10) REVERT: C 829 PHE cc_start: 0.7441 (m-80) cc_final: 0.6994 (p90) REVERT: C 850 ASP cc_start: 0.8416 (t0) cc_final: 0.8093 (t0) REVERT: C 883 LYS cc_start: 0.9112 (mttm) cc_final: 0.8870 (mmtp) REVERT: C 898 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7419 (tpp80) REVERT: C 925 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8343 (tt0) REVERT: C 928 MET cc_start: 0.8733 (tpp) cc_final: 0.8131 (tpp) REVERT: C 938 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8297 (tpm-80) REVERT: C 1141 LYS cc_start: 0.8743 (mttt) cc_final: 0.8307 (mtpt) REVERT: C 1152 GLU cc_start: 0.8361 (tp30) cc_final: 0.7643 (tp30) REVERT: C 1155 ASN cc_start: 0.8760 (m-40) cc_final: 0.8154 (t0) REVERT: C 1244 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8218 (mp0) REVERT: C 1331 MET cc_start: 0.7191 (tpp) cc_final: 0.6367 (tpt) outliers start: 106 outliers final: 86 residues processed: 648 average time/residue: 0.1875 time to fit residues: 204.5180 Evaluate side-chains 644 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 552 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.0070 chunk 127 optimal weight: 8.9990 chunk 280 optimal weight: 7.9990 chunk 344 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 179 optimal weight: 0.2980 chunk 348 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 583 GLN B 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.170609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.126585 restraints weight = 52022.621| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.96 r_work: 0.3455 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33048 Z= 0.143 Angle : 0.761 13.137 45426 Z= 0.350 Chirality : 0.047 0.332 5778 Planarity : 0.003 0.056 5376 Dihedral : 5.660 29.009 4014 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 3.42 % Allowed : 21.69 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.14), residues: 3717 helix: 1.14 (0.20), residues: 747 sheet: -1.65 (0.17), residues: 912 loop : -2.74 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 977 TYR 0.031 0.001 TYR C1067 PHE 0.030 0.001 PHE B 293 TRP 0.046 0.001 TRP B 222 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (32790) covalent geometry : angle 0.68150 / 0.33 (44703) SS BOND : bond 0.00449 / 0.31 ( 42) SS BOND : angle 1.79819 / 1.27 ( 84) hydrogen bonds : bond 0.03516 / 2.48 ( 851) hydrogen bonds : angle 4.88800 / 3.38 ( 2427) Misc. bond : bond 0.00096 / 0.05 ( 3) link_ALPHA1-2 : bond 0.00802 / 0.40 ( 6) link_ALPHA1-2 : angle 1.52070 / 0.86 ( 18) link_ALPHA1-3 : bond 0.00558 / 0.26 ( 12) link_ALPHA1-3 : angle 3.11119 / 1.98 ( 36) link_ALPHA1-6 : bond 0.00789 / 0.52 ( 24) link_ALPHA1-6 : angle 1.50122 / 1.05 ( 72) link_BETA1-4 : bond 0.00911 / 0.64 ( 87) link_BETA1-4 : angle 2.41284 / 1.66 ( 261) link_BETA1-6 : bond 0.00388 / 0.19 ( 3) link_BETA1-6 : angle 1.21439 / 0.75 ( 9) link_NAG-ASN : bond 0.00577 / 0.38 ( 81) link_NAG-ASN : angle 3.62980 / 2.29 ( 243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 550 time to evaluate : 1.144 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: A 286 ASP cc_start: 0.8598 (t70) cc_final: 0.8224 (t0) REVERT: A 293 PHE cc_start: 0.8654 (t80) cc_final: 0.7761 (t80) REVERT: A 371 ASP cc_start: 0.7044 (p0) cc_final: 0.6261 (m-30) REVERT: A 372 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: A 382 THR cc_start: 0.8049 (m) cc_final: 0.7704 (t) REVERT: A 461 LYS cc_start: 0.8924 (tttt) cc_final: 0.8592 (tttt) REVERT: A 477 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7709 (p) REVERT: A 623 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: A 664 TRP cc_start: 0.6786 (m-10) cc_final: 0.6242 (m100) REVERT: A 680 MET cc_start: 0.8218 (mmt) cc_final: 0.7556 (mtp) REVERT: A 702 CYS cc_start: 0.7769 (m) cc_final: 0.7483 (m) REVERT: A 824 ILE cc_start: 0.8796 (mm) cc_final: 0.8515 (tp) REVERT: A 829 PHE cc_start: 0.7518 (m-80) cc_final: 0.7071 (p90) REVERT: A 833 ASN cc_start: 0.9035 (t0) cc_final: 0.8825 (t0) REVERT: A 898 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7514 (tpp80) REVERT: A 925 GLU cc_start: 0.8914 (tt0) cc_final: 0.8360 (tt0) REVERT: A 928 MET cc_start: 0.8639 (tpp) cc_final: 0.8054 (tpp) REVERT: A 1023 VAL cc_start: 0.9483 (t) cc_final: 0.9031 (m) REVERT: A 1059 MET cc_start: 0.8738 (ttm) cc_final: 0.8508 (ttm) REVERT: A 1141 LYS cc_start: 0.8848 (mttt) cc_final: 0.8398 (mtpt) REVERT: A 1152 GLU cc_start: 0.8390 (tp30) cc_final: 0.7692 (tp30) REVERT: A 1155 ASN cc_start: 0.8741 (m-40) cc_final: 0.8076 (t0) REVERT: A 1260 TYR cc_start: 0.7790 (m-10) cc_final: 0.7520 (m-10) REVERT: B 247 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7252 (mtt90) REVERT: B 286 ASP cc_start: 0.8686 (t70) cc_final: 0.8130 (t0) REVERT: B 371 ASP cc_start: 0.7006 (p0) cc_final: 0.6403 (m-30) REVERT: B 372 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: B 382 THR cc_start: 0.8085 (m) cc_final: 0.7785 (t) REVERT: B 583 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7830 (mm-40) REVERT: B 633 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8020 (mm-40) REVERT: B 657 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8151 (p) REVERT: B 680 MET cc_start: 0.8499 (mmm) cc_final: 0.8039 (mtp) REVERT: B 702 CYS cc_start: 0.7749 (m) cc_final: 0.7359 (m) REVERT: B 775 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: B 805 GLN cc_start: 0.8753 (mt0) cc_final: 0.8440 (mp10) REVERT: B 822 SER cc_start: 0.8867 (m) cc_final: 0.8565 (t) REVERT: B 824 ILE cc_start: 0.8737 (mm) cc_final: 0.8472 (tp) REVERT: B 829 PHE cc_start: 0.7376 (m-80) cc_final: 0.7028 (p90) REVERT: B 925 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8385 (tt0) REVERT: B 1059 MET cc_start: 0.8612 (ttm) cc_final: 0.8336 (ttm) REVERT: B 1066 ASN cc_start: 0.8839 (m110) cc_final: 0.8525 (m110) REVERT: B 1076 GLN cc_start: 0.8146 (mp10) cc_final: 0.7917 (mp10) REVERT: B 1120 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8347 (mttt) REVERT: B 1152 GLU cc_start: 0.8295 (tp30) cc_final: 0.7734 (tp30) REVERT: B 1155 ASN cc_start: 0.8704 (m-40) cc_final: 0.8079 (t0) REVERT: B 1158 GLU cc_start: 0.7557 (tt0) cc_final: 0.7289 (tt0) REVERT: B 1161 GLU cc_start: 0.7567 (pm20) cc_final: 0.7205 (pm20) REVERT: C 286 ASP cc_start: 0.8675 (t70) cc_final: 0.8412 (t0) REVERT: C 293 PHE cc_start: 0.8646 (t80) cc_final: 0.8028 (t80) REVERT: C 371 ASP cc_start: 0.6912 (p0) cc_final: 0.6521 (m-30) REVERT: C 382 THR cc_start: 0.7938 (m) cc_final: 0.7713 (t) REVERT: C 444 ASP cc_start: 0.8510 (p0) cc_final: 0.8299 (p0) REVERT: C 657 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8215 (p) REVERT: C 663 LYS cc_start: 0.8838 (tttt) cc_final: 0.8604 (tppp) REVERT: C 664 TRP cc_start: 0.7013 (m-10) cc_final: 0.6480 (m100) REVERT: C 711 GLN cc_start: 0.8754 (tt0) cc_final: 0.8220 (mt0) REVERT: C 805 GLN cc_start: 0.8689 (mt0) cc_final: 0.8316 (mp10) REVERT: C 829 PHE cc_start: 0.7470 (m-80) cc_final: 0.6971 (p90) REVERT: C 850 ASP cc_start: 0.8460 (t0) cc_final: 0.8162 (t0) REVERT: C 883 LYS cc_start: 0.9120 (mttm) cc_final: 0.8867 (mmtp) REVERT: C 898 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7484 (tpp80) REVERT: C 925 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8344 (tt0) REVERT: C 928 MET cc_start: 0.8733 (tpp) cc_final: 0.8111 (tpp) REVERT: C 938 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8320 (tpm-80) REVERT: C 1076 GLN cc_start: 0.7905 (mp10) cc_final: 0.7037 (tp40) REVERT: C 1141 LYS cc_start: 0.8772 (mttt) cc_final: 0.8332 (mtpt) REVERT: C 1152 GLU cc_start: 0.8404 (tp30) cc_final: 0.7710 (tp30) REVERT: C 1155 ASN cc_start: 0.8803 (m-40) cc_final: 0.8110 (t0) REVERT: C 1266 ASP cc_start: 0.8542 (t0) cc_final: 0.8323 (t0) outliers start: 112 outliers final: 93 residues processed: 618 average time/residue: 0.1835 time to fit residues: 192.1703 Evaluate side-chains 637 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 535 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1293 MET Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 668 PHE Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 368 optimal weight: 2.9990 chunk 369 optimal weight: 5.9990 chunk 365 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 364 optimal weight: 0.9990 chunk 159 optimal weight: 0.0870 chunk 170 optimal weight: 0.0770 chunk 319 optimal weight: 0.7980 chunk 336 optimal weight: 0.1980 chunk 219 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.173205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.129373 restraints weight = 52361.152| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 4.00 r_work: 0.3492 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33048 Z= 0.118 Angle : 0.741 13.166 45426 Z= 0.342 Chirality : 0.047 0.329 5778 Planarity : 0.003 0.047 5376 Dihedral : 5.539 28.188 4014 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 3.02 % Allowed : 22.40 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.14), residues: 3717 helix: 1.33 (0.20), residues: 732 sheet: -1.50 (0.18), residues: 843 loop : -2.68 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 977 TYR 0.024 0.001 TYR B 625 PHE 0.024 0.001 PHE B 293 TRP 0.041 0.002 TRP B 222 HIS 0.004 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (32790) covalent geometry : angle 0.66322 / 0.32 (44703) SS BOND : bond 0.00397 / 0.28 ( 42) SS BOND : angle 1.59350 / 1.14 ( 84) hydrogen bonds : bond 0.03269 / 2.31 ( 851) hydrogen bonds : angle 4.78841 / 3.30 ( 2427) Misc. bond : bond 0.00041 / 0.02 ( 3) link_ALPHA1-2 : bond 0.00798 / 0.40 ( 6) link_ALPHA1-2 : angle 1.51891 / 0.85 ( 18) link_ALPHA1-3 : bond 0.00552 / 0.26 ( 12) link_ALPHA1-3 : angle 2.99089 / 1.90 ( 36) link_ALPHA1-6 : bond 0.00820 / 0.54 ( 24) link_ALPHA1-6 : angle 1.51409 / 1.05 ( 72) link_BETA1-4 : bond 0.00946 / 0.66 ( 87) link_BETA1-4 : angle 2.35185 / 1.61 ( 261) link_BETA1-6 : bond 0.00424 / 0.21 ( 3) link_BETA1-6 : angle 1.20948 / 0.75 ( 9) link_NAG-ASN : bond 0.00623 / 0.42 ( 81) link_NAG-ASN : angle 3.54574 / 2.24 ( 243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 559 time to evaluate : 1.156 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: A 247 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7437 (mtt90) REVERT: A 286 ASP cc_start: 0.8603 (t70) cc_final: 0.8159 (t0) REVERT: A 293 PHE cc_start: 0.8620 (t80) cc_final: 0.7718 (t80) REVERT: A 371 ASP cc_start: 0.7051 (p0) cc_final: 0.6309 (m-30) REVERT: A 372 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: A 382 THR cc_start: 0.7887 (m) cc_final: 0.7544 (t) REVERT: A 477 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7588 (p) REVERT: A 657 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8189 (p) REVERT: A 664 TRP cc_start: 0.6829 (m-10) cc_final: 0.6252 (m100) REVERT: A 680 MET cc_start: 0.8169 (mmt) cc_final: 0.7663 (mtp) REVERT: A 702 CYS cc_start: 0.7683 (m) cc_final: 0.7432 (m) REVERT: A 711 GLN cc_start: 0.8680 (tt0) cc_final: 0.8068 (mt0) REVERT: A 824 ILE cc_start: 0.8755 (mm) cc_final: 0.8469 (tp) REVERT: A 829 PHE cc_start: 0.7486 (m-80) cc_final: 0.7076 (p90) REVERT: A 883 LYS cc_start: 0.8983 (mmtp) cc_final: 0.8649 (pttp) REVERT: A 898 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7488 (tpp80) REVERT: A 925 GLU cc_start: 0.8919 (tt0) cc_final: 0.8382 (tt0) REVERT: A 928 MET cc_start: 0.8607 (tpp) cc_final: 0.8007 (tpp) REVERT: A 1023 VAL cc_start: 0.9430 (t) cc_final: 0.9032 (m) REVERT: A 1059 MET cc_start: 0.8719 (ttm) cc_final: 0.8484 (ttm) REVERT: A 1141 LYS cc_start: 0.8755 (mttt) cc_final: 0.8302 (mtpt) REVERT: A 1152 GLU cc_start: 0.8324 (tp30) cc_final: 0.7611 (tp30) REVERT: A 1155 ASN cc_start: 0.8769 (m-40) cc_final: 0.8114 (t0) REVERT: A 1204 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7916 (tt0) REVERT: A 1260 TYR cc_start: 0.7772 (m-10) cc_final: 0.7516 (m-10) REVERT: B 184 PHE cc_start: 0.6898 (m-80) cc_final: 0.6521 (m-80) REVERT: B 247 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7389 (mtm180) REVERT: B 286 ASP cc_start: 0.8678 (t70) cc_final: 0.8044 (t0) REVERT: B 371 ASP cc_start: 0.6888 (p0) cc_final: 0.6346 (m-30) REVERT: B 372 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: B 382 THR cc_start: 0.7945 (m) cc_final: 0.7625 (t) REVERT: B 583 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7834 (mm-40) REVERT: B 633 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7964 (mm-40) REVERT: B 657 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8143 (p) REVERT: B 664 TRP cc_start: 0.7119 (m100) cc_final: 0.6893 (m100) REVERT: B 680 MET cc_start: 0.8391 (mmm) cc_final: 0.7914 (mtp) REVERT: B 702 CYS cc_start: 0.7689 (m) cc_final: 0.7300 (m) REVERT: B 775 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: B 805 GLN cc_start: 0.8779 (mt0) cc_final: 0.8442 (mp10) REVERT: B 822 SER cc_start: 0.8889 (m) cc_final: 0.8590 (t) REVERT: B 824 ILE cc_start: 0.8685 (mm) cc_final: 0.8433 (tp) REVERT: B 829 PHE cc_start: 0.7260 (m-80) cc_final: 0.7020 (p90) REVERT: B 925 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8382 (tt0) REVERT: B 1000 TYR cc_start: 0.8398 (m-80) cc_final: 0.8123 (m-80) REVERT: B 1059 MET cc_start: 0.8580 (ttm) cc_final: 0.8309 (ttm) REVERT: B 1066 ASN cc_start: 0.8755 (m110) cc_final: 0.8449 (m110) REVERT: B 1152 GLU cc_start: 0.8251 (tp30) cc_final: 0.7669 (tp30) REVERT: B 1155 ASN cc_start: 0.8659 (m-40) cc_final: 0.8096 (t0) REVERT: B 1158 GLU cc_start: 0.7507 (tt0) cc_final: 0.7231 (tt0) REVERT: B 1161 GLU cc_start: 0.7560 (pm20) cc_final: 0.7196 (pm20) REVERT: C 286 ASP cc_start: 0.8683 (t70) cc_final: 0.8372 (t0) REVERT: C 293 PHE cc_start: 0.8595 (t80) cc_final: 0.7971 (t80) REVERT: C 371 ASP cc_start: 0.6840 (p0) cc_final: 0.6298 (m-30) REVERT: C 382 THR cc_start: 0.7862 (m) cc_final: 0.7604 (t) REVERT: C 444 ASP cc_start: 0.8481 (p0) cc_final: 0.8260 (p0) REVERT: C 529 LYS cc_start: 0.8309 (mmmm) cc_final: 0.7770 (mmmm) REVERT: C 641 GLU cc_start: 0.8115 (tp30) cc_final: 0.7833 (tp30) REVERT: C 657 SER cc_start: 0.8637 (OUTLIER) cc_final: 0.8222 (p) REVERT: C 663 LYS cc_start: 0.8788 (tttt) cc_final: 0.8581 (tppp) REVERT: C 664 TRP cc_start: 0.7045 (m-10) cc_final: 0.6532 (m100) REVERT: C 680 MET cc_start: 0.8410 (mmm) cc_final: 0.7990 (mtp) REVERT: C 711 GLN cc_start: 0.8726 (tt0) cc_final: 0.8230 (mt0) REVERT: C 805 GLN cc_start: 0.8687 (mt0) cc_final: 0.8390 (mp10) REVERT: C 829 PHE cc_start: 0.7428 (m-80) cc_final: 0.7001 (p90) REVERT: C 883 LYS cc_start: 0.9076 (mttm) cc_final: 0.8851 (mmtp) REVERT: C 898 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7416 (tpp80) REVERT: C 925 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8375 (tt0) REVERT: C 928 MET cc_start: 0.8724 (tpp) cc_final: 0.8120 (tpp) REVERT: C 938 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8346 (tpm-80) REVERT: C 1141 LYS cc_start: 0.8743 (mttt) cc_final: 0.8327 (mtpt) REVERT: C 1155 ASN cc_start: 0.8720 (m-40) cc_final: 0.7999 (t0) REVERT: C 1244 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8184 (mp0) REVERT: C 1266 ASP cc_start: 0.8508 (t0) cc_final: 0.8283 (t0) REVERT: C 1331 MET cc_start: 0.6905 (tpp) cc_final: 0.6145 (tpt) outliers start: 99 outliers final: 80 residues processed: 618 average time/residue: 0.1809 time to fit residues: 188.7562 Evaluate side-chains 625 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 535 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 775 GLN Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1293 MET Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 286 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 209 optimal weight: 0.6980 chunk 250 optimal weight: 0.5980 chunk 216 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.172990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.129084 restraints weight = 52199.027| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.99 r_work: 0.3490 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33048 Z= 0.121 Angle : 0.737 12.690 45426 Z= 0.340 Chirality : 0.046 0.324 5778 Planarity : 0.003 0.049 5376 Dihedral : 5.444 27.753 4014 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 2.90 % Allowed : 22.55 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.14), residues: 3717 helix: 1.34 (0.20), residues: 732 sheet: -1.47 (0.18), residues: 843 loop : -2.66 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 977 TYR 0.026 0.001 TYR C1067 PHE 0.024 0.001 PHE B 293 TRP 0.040 0.001 TRP C 222 HIS 0.003 0.000 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (32790) covalent geometry : angle 0.66171 / 0.32 (44703) SS BOND : bond 0.00370 / 0.26 ( 42) SS BOND : angle 1.51867 / 1.10 ( 84) hydrogen bonds : bond 0.03254 / 2.30 ( 851) hydrogen bonds : angle 4.76912 / 3.29 ( 2427) Misc. bond : bond 0.00054 / 0.03 ( 3) link_ALPHA1-2 : bond 0.00771 / 0.39 ( 6) link_ALPHA1-2 : angle 1.50549 / 0.85 ( 18) link_ALPHA1-3 : bond 0.00542 / 0.25 ( 12) link_ALPHA1-3 : angle 2.92965 / 1.86 ( 36) link_ALPHA1-6 : bond 0.00815 / 0.53 ( 24) link_ALPHA1-6 : angle 1.49481 / 1.04 ( 72) link_BETA1-4 : bond 0.00933 / 0.65 ( 87) link_BETA1-4 : angle 2.34404 / 1.61 ( 261) link_BETA1-6 : bond 0.00410 / 0.21 ( 3) link_BETA1-6 : angle 1.21446 / 0.76 ( 9) link_NAG-ASN : bond 0.00590 / 0.39 ( 81) link_NAG-ASN : angle 3.48396 / 2.20 ( 243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9078.59 seconds wall clock time: 156 minutes 31.77 seconds (9391.77 seconds total)