Starting phenix.real_space_refine on Mon Jul 6 00:07:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w6m_32329/07_2026/7w6m_32329.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6m_32329/07_2026/7w6m_32329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w6m_32329/07_2026/7w6m_32329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6m_32329/07_2026/7w6m_32329.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7w6m_32329/07_2026/7w6m_32329.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w6m_32329/07_2026/7w6m_32329.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w6m_32329/07_2026/7w6m_32329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6m_32329/07_2026/7w6m_32329.map" } resolution = 4.7 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= 0.001 sd= 0.061 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 123 5.16 5 C 19362 2.51 5 N 4776 2.21 5 O 6495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30756 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 9400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9400 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 45, 'TRANS': 1178} Chain: "B" Number of atoms: 9400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9400 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 45, 'TRANS': 1178} Chain: "C" Number of atoms: 9400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9400 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 45, 'TRANS': 1178} Chain: "D" 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: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 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: "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: 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: 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: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, '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: 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: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 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: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 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: "T" 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: "U" 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: "V" 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: "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: 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: "Z" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, '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: "a" 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: "b" 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: "c" 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: "d" 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: "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: 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: "g" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 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: "i" 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: "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: 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: "l" 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: "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: 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: "o" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, '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: "p" 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: "q" 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: "r" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "v" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.64, per 1000 atoms: 0.22 Number of scatterers: 30756 At special positions: 0 Unit cell: (147, 151.2, 183.4, 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 123 16.00 O 6495 8.00 N 4776 7.00 C 19362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.03 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.03 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " 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=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 4 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA T 3 " - " MAN T 5 " " BMA Y 3 " - " MAN Y 5 " " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 5 " " BMA n 3 " - " MAN n 5 " " BMA p 3 " - " MAN p 5 " " BMA q 3 " - " MAN q 5 " " BMA r 3 " - " MAN r 5 " " BMA s 3 " - " MAN s 5 " " BMA u 3 " - " MAN u 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " 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 c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " 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 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 n 2 " - " BMA n 3 " " 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 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 u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 4 " " NAG K 1 " - " FUC K 5 " " NAG R 1 " - " FUC R 3 " " NAG S 1 " - " FUC S 4 " " NAG U 1 " - " FUC U 4 " " NAG Z 1 " - " FUC Z 5 " " NAG g 1 " - " FUC g 3 " " NAG h 1 " - " FUC h 4 " " NAG j 1 " - " FUC j 4 " " NAG o 1 " - " FUC o 5 " " NAG v 1 " - " FUC v 3 " NAG-ASN " NAG A1401 " - " ASN A 118 " " NAG A1402 " - " ASN A 425 " " NAG A1403 " - " ASN A 667 " " NAG A1404 " - " ASN A 351 " " NAG A1405 " - " ASN A1249 " " NAG A1406 " - " ASN A1009 " " NAG B1401 " - " ASN B 118 " " NAG B1402 " - " ASN B 425 " " NAG B1403 " - " ASN B 667 " " NAG B1404 " - " ASN B 351 " " NAG B1405 " - " ASN B1249 " " NAG B1406 " - " ASN B1009 " " NAG C1401 " - " ASN C 118 " " NAG C1402 " - " ASN C 425 " " NAG C1403 " - " ASN C 667 " " NAG C1404 " - " ASN C 351 " " NAG C1405 " - " ASN C1249 " " NAG C1406 " - " ASN C1009 " " NAG D 1 " - " ASN A 216 " " NAG E 1 " - " ASN A 264 " " NAG F 1 " - " ASN A 300 " " NAG G 1 " - " ASN A 324 " " NAG H 1 " - " ASN A 344 " " NAG I 1 " - " ASN A 381 " " NAG J 1 " - " ASN A 514 " " NAG K 1 " - " ASN A 556 " " NAG L 1 " - " ASN A 688 " " NAG M 1 " - " ASN A 726 " " NAG N 1 " - " ASN A 781 " " NAG O 1 " - " ASN A 787 " " NAG P 1 " - " ASN A 873 " " NAG Q 1 " - " ASN A1232 " " NAG R 1 " - " ASN A 743 " " NAG S 1 " - " ASN B 216 " " NAG T 1 " - " ASN B 264 " " NAG U 1 " - " ASN B 300 " " NAG V 1 " - " ASN B 324 " " NAG W 1 " - " ASN B 344 " " NAG X 1 " - " ASN B 381 " " NAG Y 1 " - " ASN B 514 " " NAG Z 1 " - " ASN B 556 " " NAG a 1 " - " ASN B 688 " " NAG b 1 " - " ASN B 726 " " NAG c 1 " - " ASN B 781 " " NAG d 1 " - " ASN B 787 " " NAG e 1 " - " ASN B 873 " " NAG f 1 " - " ASN B1232 " " NAG g 1 " - " ASN B 743 " " NAG h 1 " - " ASN C 216 " " NAG i 1 " - " ASN C 264 " " NAG j 1 " - " ASN C 300 " " NAG k 1 " - " ASN C 324 " " NAG l 1 " - " ASN C 344 " " NAG m 1 " - " ASN C 381 " " NAG n 1 " - " ASN C 514 " " NAG o 1 " - " ASN C 556 " " NAG p 1 " - " ASN C 688 " " NAG q 1 " - " ASN C 726 " " NAG r 1 " - " ASN C 781 " " NAG s 1 " - " ASN C 787 " " NAG t 1 " - " ASN C 873 " " NAG u 1 " - " ASN C1232 " " NAG v 1 " - " ASN C 743 " Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 931.5 milliseconds 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6804 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 50 sheets defined 24.5% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.798A pdb=" N THR A 120 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 325 through 332 removed outlier: 4.260A pdb=" N ILE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.508A pdb=" N PHE A 360 " --> pdb=" O HIS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 466 through 475 removed outlier: 3.604A pdb=" N GLN A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.733A pdb=" N LYS A 820 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 852 removed outlier: 3.659A pdb=" N LEU A 852 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 917 through 923 removed outlier: 3.715A pdb=" N SER A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 937 removed outlier: 3.622A pdb=" N ALA A 932 " --> pdb=" O ASP A 928 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 933 " --> pdb=" O LEU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 959 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.519A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1014 Processing helix chain 'A' and resid 1016 through 1020 removed outlier: 3.631A pdb=" N ALA A1020 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1047 removed outlier: 3.770A pdb=" N ASN A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1058 removed outlier: 4.101A pdb=" N THR A1053 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1049 through 1058' Processing helix chain 'A' and resid 1066 through 1072 Processing helix chain 'A' and resid 1075 through 1123 removed outlier: 3.939A pdb=" N GLU A1107 " --> pdb=" O THR A1103 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A1123 " --> pdb=" O VAL A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1198 removed outlier: 4.382A pdb=" N HIS A1197 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1237 through 1242 Processing helix chain 'A' and resid 1247 through 1254 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.833A pdb=" N THR B 120 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.502A pdb=" N GLY B 292 " --> pdb=" O LYS B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 removed outlier: 4.254A pdb=" N ILE B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.513A pdb=" N PHE B 360 " --> pdb=" O HIS B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 removed outlier: 3.902A pdb=" N ASP B 433 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP B 434 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.740A pdb=" N LYS B 820 " --> pdb=" O ASN B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 852 removed outlier: 3.750A pdb=" N LEU B 852 " --> pdb=" O VAL B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 862 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.723A pdb=" N SER B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 937 removed outlier: 3.615A pdb=" N ALA B 932 " --> pdb=" O ASP B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 959 Processing helix chain 'B' and resid 973 through 986 removed outlier: 3.527A pdb=" N ALA B 977 " --> pdb=" O PRO B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1014 Processing helix chain 'B' and resid 1016 through 1020 removed outlier: 3.636A pdb=" N ALA B1020 " --> pdb=" O VAL B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1047 removed outlier: 3.760A pdb=" N ASN B1043 " --> pdb=" O GLN B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1058 removed outlier: 4.098A pdb=" N THR B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B1055 " --> pdb=" O GLN B1051 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B1057 " --> pdb=" O THR B1053 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS B1058 " --> pdb=" O VAL B1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1049 through 1058' Processing helix chain 'B' and resid 1066 through 1072 Processing helix chain 'B' and resid 1075 through 1122 removed outlier: 3.948A pdb=" N GLU B1107 " --> pdb=" O THR B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1198 removed outlier: 4.382A pdb=" N HIS B1197 " --> pdb=" O LEU B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'B' and resid 1237 through 1242 Processing helix chain 'B' and resid 1247 through 1254 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.800A pdb=" N THR C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.673A pdb=" N GLY C 292 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 332 removed outlier: 4.234A pdb=" N ILE C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.502A pdb=" N PHE C 360 " --> pdb=" O HIS C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 436 removed outlier: 3.907A pdb=" N ASP C 433 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP C 434 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 577 through 581 Processing helix chain 'C' and resid 807 through 813 Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.723A pdb=" N LYS C 820 " --> pdb=" O ASN C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 852 removed outlier: 3.732A pdb=" N LEU C 852 " --> pdb=" O VAL C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 862 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 917 through 923 removed outlier: 3.723A pdb=" N SER C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 923 " --> pdb=" O ARG C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 937 removed outlier: 3.621A pdb=" N ALA C 932 " --> pdb=" O ASP C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 959 Processing helix chain 'C' and resid 973 through 986 removed outlier: 3.508A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1014 Processing helix chain 'C' and resid 1016 through 1020 removed outlier: 3.624A pdb=" N ALA C1020 " --> pdb=" O VAL C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1047 removed outlier: 3.755A pdb=" N ASN C1043 " --> pdb=" O GLN C1039 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1058 removed outlier: 4.111A pdb=" N THR C1053 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C1054 " --> pdb=" O THR C1050 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN C1055 " --> pdb=" O GLN C1051 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU C1056 " --> pdb=" O LEU C1052 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN C1057 " --> pdb=" O THR C1053 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS C1058 " --> pdb=" O VAL C1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1049 through 1058' Processing helix chain 'C' and resid 1066 through 1072 Processing helix chain 'C' and resid 1075 through 1122 removed outlier: 3.957A pdb=" N GLU C1107 " --> pdb=" O THR C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1194 through 1198 removed outlier: 4.385A pdb=" N HIS C1197 " --> pdb=" O LEU C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'C' and resid 1237 through 1242 Processing helix chain 'C' and resid 1247 through 1254 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 184 removed outlier: 3.596A pdb=" N TYR A 181 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 154 removed outlier: 4.869A pdb=" N LEU A 107 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.337A pdb=" N ASN A 445 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 281 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 443 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS A 283 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 441 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 285 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP A 439 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN A 322 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE A 441 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 320 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER A 443 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA A 318 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.337A pdb=" N ASN A 445 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 281 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 443 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS A 283 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 441 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 285 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP A 439 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 462 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU A 452 " --> pdb=" O ARG A 460 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 460 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLN A 454 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 298 removed outlier: 4.494A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 388 " --> pdb=" O CYS A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 488 removed outlier: 6.987A pdb=" N VAL A 709 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 716 " --> pdb=" O HIS A 737 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 removed outlier: 4.165A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 532 through 536 removed outlier: 6.737A pdb=" N TYR A 619 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL A 590 " --> pdb=" O TYR A 619 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A 621 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 588 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR A 623 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY A 625 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER A 584 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 532 through 536 removed outlier: 7.308A pdb=" N LEU A 603 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 617 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A 601 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 619 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS A 599 " --> pdb=" O TYR A 619 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 786 removed outlier: 4.244A pdb=" N GLY A 780 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 782 " --> pdb=" O VAL A1166 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A1166 " --> pdb=" O ILE A 782 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 797 removed outlier: 4.135A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A1158 " --> pdb=" O HIS A1139 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N HIS A1139 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB6, first strand: chain 'A' and resid 1220 through 1223 Processing sheet with id=AB7, first strand: chain 'A' and resid 1187 through 1191 Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 51 Processing sheet with id=AB9, first strand: chain 'B' and resid 181 through 184 removed outlier: 3.757A pdb=" N TYR B 181 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 175 " --> pdb=" O TYR B 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 148 through 154 removed outlier: 4.872A pdb=" N LEU B 107 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 270 through 286 removed outlier: 3.516A pdb=" N SER B 275 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 449 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASN B 445 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 281 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER B 443 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS B 283 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 441 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 285 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP B 439 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 322 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE B 441 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG B 320 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER B 443 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA B 318 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 270 through 286 removed outlier: 3.516A pdb=" N SER B 275 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 449 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASN B 445 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 281 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER B 443 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS B 283 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 441 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 285 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP B 439 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 462 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU B 452 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ARG B 460 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLN B 454 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 295 through 298 removed outlier: 4.502A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 388 " --> pdb=" O CYS B 373 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 483 through 488 removed outlier: 6.993A pdb=" N VAL B 709 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 716 " --> pdb=" O HIS B 737 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 499 through 502 removed outlier: 4.157A pdb=" N VAL B 694 " --> pdb=" O THR B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 532 through 536 removed outlier: 6.739A pdb=" N TYR B 619 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B 590 " --> pdb=" O TYR B 619 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN B 621 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE B 588 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR B 623 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 625 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER B 584 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 532 through 536 removed outlier: 7.306A pdb=" N LEU B 603 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER B 617 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 601 " --> pdb=" O SER B 617 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR B 619 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS B 599 " --> pdb=" O TYR B 619 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AD1, first strand: chain 'B' and resid 781 through 786 removed outlier: 3.684A pdb=" N ILE B 782 " --> pdb=" O VAL B1166 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B1166 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 789 through 797 removed outlier: 4.131A pdb=" N PHE B1141 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU B1158 " --> pdb=" O HIS B1139 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS B1139 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AD4, first strand: chain 'B' and resid 880 through 883 removed outlier: 6.491A pdb=" N SER B 881 " --> pdb=" O LYS B 893 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS B 893 " --> pdb=" O SER B 881 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 883 " --> pdb=" O VAL B 891 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1220 through 1223 Processing sheet with id=AD6, first strand: chain 'B' and resid 1187 through 1191 Processing sheet with id=AD7, first strand: chain 'C' and resid 46 through 51 Processing sheet with id=AD8, first strand: chain 'C' and resid 180 through 184 removed outlier: 3.601A pdb=" N TYR C 181 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 148 through 154 removed outlier: 4.880A pdb=" N LEU C 107 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 270 through 286 removed outlier: 3.534A pdb=" N SER C 275 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 449 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN C 445 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 281 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 443 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS C 283 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 441 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 285 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP C 439 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN C 322 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE C 441 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG C 320 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER C 443 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA C 318 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 270 through 286 removed outlier: 3.534A pdb=" N SER C 275 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 449 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN C 445 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 281 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 443 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS C 283 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 441 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 285 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP C 439 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 462 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 452 " --> pdb=" O ARG C 460 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ARG C 460 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN C 454 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 295 through 298 removed outlier: 4.501A pdb=" N ILE C 335 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 388 " --> pdb=" O CYS C 373 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 483 through 488 removed outlier: 6.802A pdb=" N VAL C 709 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE C 713 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 716 " --> pdb=" O HIS C 737 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 499 through 502 removed outlier: 4.167A pdb=" N VAL C 694 " --> pdb=" O THR C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 532 through 536 removed outlier: 6.738A pdb=" N TYR C 619 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL C 590 " --> pdb=" O TYR C 619 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 621 " --> pdb=" O PHE C 588 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE C 588 " --> pdb=" O GLN C 621 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR C 623 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY C 625 " --> pdb=" O SER C 584 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER C 584 " --> pdb=" O GLY C 625 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 532 through 536 removed outlier: 7.304A pdb=" N LEU C 603 " --> pdb=" O PHE C 615 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER C 617 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE C 601 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR C 619 " --> pdb=" O CYS C 599 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS C 599 " --> pdb=" O TYR C 619 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AE9, first strand: chain 'C' and resid 781 through 786 removed outlier: 3.673A pdb=" N ILE C 782 " --> pdb=" O VAL C1166 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C1166 " --> pdb=" O ILE C 782 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 789 through 797 removed outlier: 4.127A pdb=" N PHE C1141 " --> pdb=" O THR C1156 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU C1158 " --> pdb=" O HIS C1139 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS C1139 " --> pdb=" O LEU C1158 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AF3, first strand: chain 'C' and resid 880 through 883 removed outlier: 6.496A pdb=" N SER C 881 " --> pdb=" O LYS C 893 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS C 893 " --> pdb=" O SER C 881 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 883 " --> pdb=" O VAL C 891 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1220 through 1223 Processing sheet with id=AF5, first strand: chain 'C' and resid 1187 through 1191 1167 hydrogen bonds defined for protein. 3180 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: 6.59 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9399 1.34 - 1.46: 7875 1.46 - 1.58: 13959 1.58 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 31386 Sorted by residual: bond pdb=" C1 NAG C1403 " pdb=" O5 NAG C1403 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1 NAG B1403 " pdb=" O5 NAG B1403 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1 NAG j 2 " pdb=" O5 NAG j 2 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 31381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 40517 1.58 - 3.16: 1621 3.16 - 4.74: 379 4.74 - 6.32: 222 6.32 - 7.89: 26 Bond angle restraints: 42765 Sorted by residual: angle pdb=" N VAL A 674 " pdb=" CA VAL A 674 " pdb=" C VAL A 674 " ideal model delta sigma weight residual 113.53 109.23 4.30 9.80e-01 1.04e+00 1.93e+01 angle pdb=" N GLN A 993 " pdb=" CA GLN A 993 " pdb=" CB GLN A 993 " ideal model delta sigma weight residual 114.17 109.83 4.34 1.14e+00 7.69e-01 1.45e+01 angle pdb=" N GLN B 993 " pdb=" CA GLN B 993 " pdb=" CB GLN B 993 " ideal model delta sigma weight residual 114.17 109.85 4.32 1.14e+00 7.69e-01 1.43e+01 angle pdb=" N GLN C 993 " pdb=" CA GLN C 993 " pdb=" CB GLN C 993 " ideal model delta sigma weight residual 114.17 109.89 4.28 1.14e+00 7.69e-01 1.41e+01 angle pdb=" C GLY A1135 " pdb=" N ASP A1136 " pdb=" CA ASP A1136 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.42e+00 ... (remaining 42760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 15303 16.89 - 33.79: 1356 33.79 - 50.68: 239 50.68 - 67.57: 55 67.57 - 84.46: 42 Dihedral angle restraints: 16995 sinusoidal: 6351 harmonic: 10644 Sorted by residual: dihedral pdb=" CB CYS B 464 " pdb=" SG CYS B 464 " pdb=" SG CYS B 473 " pdb=" CB CYS B 473 " ideal model delta sinusoidal sigma weight residual 93.00 164.46 -71.46 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS C 464 " pdb=" SG CYS C 464 " pdb=" SG CYS C 473 " pdb=" CB CYS C 473 " ideal model delta sinusoidal sigma weight residual 93.00 163.83 -70.83 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS A 464 " pdb=" SG CYS A 464 " pdb=" SG CYS A 473 " pdb=" CB CYS A 473 " ideal model delta sinusoidal sigma weight residual 93.00 162.49 -69.49 1 1.00e+01 1.00e-02 6.24e+01 ... (remaining 16992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 5435 0.143 - 0.286: 97 0.286 - 0.429: 12 0.429 - 0.572: 0 0.572 - 0.715: 3 Chirality restraints: 5547 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 726 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN B 726 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG q 1 " pdb=" ND2 ASN C 726 " pdb=" C2 NAG q 1 " pdb=" O5 NAG q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 5544 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 902 " -0.010 2.00e-02 2.50e+03 1.21e-02 2.55e+00 pdb=" CG PHE C 902 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 902 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 902 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 902 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 902 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 902 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 902 " 0.010 2.00e-02 2.50e+03 1.19e-02 2.48e+00 pdb=" CG PHE A 902 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 902 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 902 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 902 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 902 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 902 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 902 " 0.010 2.00e-02 2.50e+03 1.18e-02 2.43e+00 pdb=" CG PHE B 902 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE B 902 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 902 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 902 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 902 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 902 " 0.001 2.00e-02 2.50e+03 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 639 2.67 - 3.22: 29797 3.22 - 3.78: 47305 3.78 - 4.34: 60996 4.34 - 4.90: 96196 Nonbonded interactions: 234933 Sorted by model distance: nonbonded pdb=" OG1 THR A 167 " pdb=" OG1 THR A 174 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR C 167 " pdb=" OG1 THR C 174 " model vdw 2.118 3.040 nonbonded pdb=" OG1 THR B 167 " pdb=" OG1 THR B 174 " model vdw 2.157 3.040 nonbonded pdb=" O ASP B 899 " pdb=" ND2 ASN B 903 " model vdw 2.167 3.120 nonbonded pdb=" O ASP C 899 " pdb=" ND2 ASN C 903 " model vdw 2.169 3.120 ... (remaining 234928 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 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'S' selection = chain 'U' selection = chain 'h' selection = chain 'j' } ncs_group { reference = (chain 'E' and resid 1 through 4) selection = (chain 'J' and resid 1 through 4) selection = (chain 'K' and resid 1 through 4) selection = (chain 'L' and resid 1 through 4) selection = (chain 'M' and resid 1 through 4) selection = (chain 'N' and resid 1 through 4) selection = (chain 'O' and resid 1 through 4) selection = (chain 'Q' and resid 1 through 4) selection = (chain 'T' and resid 1 through 4) selection = (chain 'Y' and resid 1 through 4) selection = (chain 'Z' and resid 1 through 4) selection = (chain 'a' and resid 1 through 4) selection = (chain 'b' and resid 1 through 4) selection = (chain 'c' and resid 1 through 4) selection = (chain 'd' and resid 1 through 4) selection = (chain 'f' and resid 1 through 4) selection = (chain 'i' and resid 1 through 4) selection = (chain 'n' and resid 1 through 4) selection = (chain 'o' and resid 1 through 4) selection = (chain 'p' and resid 1 through 4) selection = (chain 'q' and resid 1 through 4) selection = (chain 'r' and resid 1 through 4) selection = (chain 's' and resid 1 through 4) selection = (chain 'u' and resid 1 through 4) } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 't' and resid 1 through 2) selection = (chain 'v' and resid 1 through 2) } ncs_group { reference = chain 'I' selection = chain 'X' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.470 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.005 0.073 31629 Z= 0.259 Angle : 0.904 16.969 43455 Z= 0.375 Chirality : 0.059 0.715 5547 Planarity : 0.003 0.031 5205 Dihedral : 13.619 84.464 10074 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.63 (0.14), residues: 3666 helix: 0.56 (0.19), residues: 783 sheet: 0.46 (0.17), residues: 924 loop : -1.30 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 146 TYR 0.012 0.001 TYR B 291 PHE 0.028 0.001 PHE C 902 TRP 0.006 0.001 TRP C 168 HIS 0.004 0.000 HIS B 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.26 (31386) covalent geometry : angle 0.83378 / 0.36 (42765) SS BOND : bond 0.00198 / 0.11 ( 39) SS BOND : angle 0.73833 / 0.55 ( 78) hydrogen bonds : bond 0.15211 / 10.57 ( 1099) hydrogen bonds : angle 6.81805 / 4.76 ( 3180) link_ALPHA1-3 : bond 0.00720 / 0.41 ( 24) link_ALPHA1-3 : angle 1.90848 / 1.42 ( 72) link_ALPHA1-6 : bond 0.00690 / 0.40 ( 21) link_ALPHA1-6 : angle 1.49858 / 1.10 ( 63) link_BETA1-4 : bond 0.01313 / 0.87 ( 84) link_BETA1-4 : angle 3.03522 / 2.14 ( 252) link_BETA1-6 : bond 0.01028 / 0.61 ( 12) link_BETA1-6 : angle 1.94687 / 1.30 ( 36) link_NAG-ASN : bond 0.00714 / 0.44 ( 63) link_NAG-ASN : angle 3.92554 / 2.91 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.7865 (m-80) cc_final: 0.7658 (m-80) REVERT: A 215 LEU cc_start: 0.9043 (mm) cc_final: 0.8768 (mm) REVERT: A 644 MET cc_start: 0.7555 (ppp) cc_final: 0.6889 (ppp) REVERT: A 1040 GLU cc_start: 0.9336 (tp30) cc_final: 0.9015 (tp30) REVERT: A 1074 LEU cc_start: 0.7872 (tt) cc_final: 0.7621 (tt) REVERT: A 1117 GLN cc_start: 0.9212 (tp-100) cc_final: 0.8944 (tp-100) REVERT: B 204 MET cc_start: 0.8714 (ppp) cc_final: 0.8431 (tmm) REVERT: B 563 TYR cc_start: 0.8965 (m-80) cc_final: 0.8713 (m-80) REVERT: B 644 MET cc_start: 0.7507 (ppp) cc_final: 0.7223 (ppp) REVERT: B 939 MET cc_start: 0.8665 (mmp) cc_final: 0.7927 (mmp) REVERT: B 1040 GLU cc_start: 0.9337 (tp30) cc_final: 0.9088 (tp30) REVERT: B 1074 LEU cc_start: 0.8464 (tt) cc_final: 0.8262 (tt) REVERT: B 1117 GLN cc_start: 0.9272 (tp-100) cc_final: 0.8953 (tp40) REVERT: C 176 PHE cc_start: 0.9038 (m-80) cc_final: 0.8711 (m-80) REVERT: C 180 ILE cc_start: 0.9230 (tp) cc_final: 0.9007 (tp) REVERT: C 181 TYR cc_start: 0.7966 (m-80) cc_final: 0.7732 (m-80) REVERT: C 563 TYR cc_start: 0.8778 (m-80) cc_final: 0.8503 (m-80) REVERT: C 644 MET cc_start: 0.7150 (ppp) cc_final: 0.6886 (ppp) REVERT: C 938 VAL cc_start: 0.9635 (t) cc_final: 0.9425 (t) REVERT: C 939 MET cc_start: 0.8872 (mmp) cc_final: 0.8125 (mmm) REVERT: C 1040 GLU cc_start: 0.9354 (tp30) cc_final: 0.9085 (tp30) REVERT: C 1117 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8775 (tp40) REVERT: C 1220 PHE cc_start: 0.9085 (m-80) cc_final: 0.8854 (m-80) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1426 time to fit residues: 55.2203 Evaluate side-chains 154 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0010 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 7.9990 overall best weight: 3.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1061 GLN ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN C1061 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.074641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.051956 restraints weight = 183277.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.053526 restraints weight = 127382.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.054598 restraints weight = 100320.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055348 restraints weight = 85629.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.055847 restraints weight = 76784.228| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31629 Z= 0.165 Angle : 0.732 15.703 43455 Z= 0.333 Chirality : 0.049 0.460 5547 Planarity : 0.003 0.026 5205 Dihedral : 3.972 19.727 3951 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % 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: -0.68 (0.14), residues: 3666 helix: 0.50 (0.18), residues: 804 sheet: 0.36 (0.17), residues: 966 loop : -1.33 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 146 TYR 0.018 0.001 TYR C 413 PHE 0.033 0.001 PHE C 902 TRP 0.006 0.001 TRP A 168 HIS 0.009 0.001 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (31386) covalent geometry : angle 0.65078 / 0.31 (42765) SS BOND : bond 0.00252 / 0.17 ( 39) SS BOND : angle 0.92858 / 0.70 ( 78) hydrogen bonds : bond 0.04785 / 3.40 ( 1099) hydrogen bonds : angle 6.02421 / 4.20 ( 3180) link_ALPHA1-3 : bond 0.00775 / 0.45 ( 24) link_ALPHA1-3 : angle 1.75491 / 1.31 ( 72) link_ALPHA1-6 : bond 0.00540 / 0.33 ( 21) link_ALPHA1-6 : angle 1.45697 / 1.07 ( 63) link_BETA1-4 : bond 0.01121 / 0.73 ( 84) link_BETA1-4 : angle 2.75111 / 1.92 ( 252) link_BETA1-6 : bond 0.01231 / 0.72 ( 12) link_BETA1-6 : angle 1.97834 / 1.31 ( 36) link_NAG-ASN : bond 0.00781 / 0.49 ( 63) link_NAG-ASN : angle 3.79535 / 2.83 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 200 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 MET cc_start: 0.7778 (ppp) cc_final: 0.7098 (ppp) REVERT: A 939 MET cc_start: 0.8784 (mmp) cc_final: 0.8282 (mmm) REVERT: A 1040 GLU cc_start: 0.9309 (tp30) cc_final: 0.9082 (tp30) REVERT: A 1074 LEU cc_start: 0.8029 (tt) cc_final: 0.7739 (tt) REVERT: A 1117 GLN cc_start: 0.9103 (tp-100) cc_final: 0.8753 (tp-100) REVERT: A 1220 PHE cc_start: 0.9129 (m-80) cc_final: 0.8810 (m-80) REVERT: B 563 TYR cc_start: 0.8926 (m-80) cc_final: 0.8702 (m-80) REVERT: B 644 MET cc_start: 0.7665 (ppp) cc_final: 0.7248 (ppp) REVERT: B 939 MET cc_start: 0.8547 (mmp) cc_final: 0.8007 (mmm) REVERT: B 1040 GLU cc_start: 0.9284 (tp30) cc_final: 0.9052 (tp30) REVERT: B 1074 LEU cc_start: 0.8433 (tt) cc_final: 0.8140 (tt) REVERT: B 1117 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8855 (tp40) REVERT: C 176 PHE cc_start: 0.9029 (m-80) cc_final: 0.8730 (m-80) REVERT: C 180 ILE cc_start: 0.9167 (tp) cc_final: 0.8952 (tp) REVERT: C 181 TYR cc_start: 0.8046 (m-80) cc_final: 0.7828 (m-80) REVERT: C 291 TYR cc_start: 0.7402 (m-80) cc_final: 0.6885 (m-80) REVERT: C 563 TYR cc_start: 0.8913 (m-80) cc_final: 0.8615 (m-80) REVERT: C 644 MET cc_start: 0.7503 (ppp) cc_final: 0.7042 (ppp) REVERT: C 939 MET cc_start: 0.8762 (mmp) cc_final: 0.8207 (mmm) REVERT: C 1040 GLU cc_start: 0.9377 (tp30) cc_final: 0.9164 (tp30) REVERT: C 1074 LEU cc_start: 0.8160 (tp) cc_final: 0.7772 (tt) REVERT: C 1117 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8623 (tp-100) REVERT: C 1220 PHE cc_start: 0.9184 (m-80) cc_final: 0.8824 (m-80) outliers start: 3 outliers final: 0 residues processed: 200 average time/residue: 0.1502 time to fit residues: 53.0137 Evaluate side-chains 152 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 362 optimal weight: 4.9990 chunk 352 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 341 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 358 optimal weight: 0.3980 chunk 246 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 313 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1029 ASN A1061 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1197 HIS B1061 GLN B1117 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1197 HIS C1029 ASN C1061 GLN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.075512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052482 restraints weight = 179968.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.054095 restraints weight = 123936.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.055196 restraints weight = 97055.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.055965 restraints weight = 82586.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.056471 restraints weight = 74013.409| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31629 Z= 0.131 Angle : 0.707 16.317 43455 Z= 0.315 Chirality : 0.049 0.473 5547 Planarity : 0.003 0.035 5205 Dihedral : 3.916 20.991 3951 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: -0.65 (0.14), residues: 3666 helix: 0.57 (0.18), residues: 807 sheet: 0.38 (0.16), residues: 981 loop : -1.35 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 146 TYR 0.012 0.001 TYR A 181 PHE 0.039 0.001 PHE C 902 TRP 0.004 0.001 TRP A 168 HIS 0.005 0.001 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (31386) covalent geometry : angle 0.62162 / 0.29 (42765) SS BOND : bond 0.00234 / 0.15 ( 39) SS BOND : angle 0.86147 / 0.65 ( 78) hydrogen bonds : bond 0.04431 / 3.13 ( 1099) hydrogen bonds : angle 5.74778 / 4.01 ( 3180) link_ALPHA1-3 : bond 0.00766 / 0.45 ( 24) link_ALPHA1-3 : angle 1.67191 / 1.26 ( 72) link_ALPHA1-6 : bond 0.00607 / 0.36 ( 21) link_ALPHA1-6 : angle 1.35675 / 1.00 ( 63) link_BETA1-4 : bond 0.01113 / 0.72 ( 84) link_BETA1-4 : angle 2.77301 / 1.94 ( 252) link_BETA1-6 : bond 0.01045 / 0.62 ( 12) link_BETA1-6 : angle 1.90472 / 1.24 ( 36) link_NAG-ASN : bond 0.00728 / 0.46 ( 63) link_NAG-ASN : angle 3.83455 / 2.84 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 PHE cc_start: 0.9028 (m-80) cc_final: 0.8811 (m-80) REVERT: A 644 MET cc_start: 0.7755 (ppp) cc_final: 0.7051 (ppp) REVERT: A 939 MET cc_start: 0.8730 (mmp) cc_final: 0.8262 (mmm) REVERT: A 1040 GLU cc_start: 0.9278 (tp30) cc_final: 0.9042 (tp30) REVERT: A 1074 LEU cc_start: 0.8061 (tt) cc_final: 0.7775 (tt) REVERT: A 1117 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8817 (tp40) REVERT: A 1220 PHE cc_start: 0.9080 (m-80) cc_final: 0.8732 (m-80) REVERT: B 291 TYR cc_start: 0.7907 (m-80) cc_final: 0.7200 (m-80) REVERT: B 644 MET cc_start: 0.7671 (ppp) cc_final: 0.7183 (ppp) REVERT: B 939 MET cc_start: 0.8422 (mmp) cc_final: 0.7913 (mmm) REVERT: B 1040 GLU cc_start: 0.9289 (tp30) cc_final: 0.9047 (tp30) REVERT: B 1074 LEU cc_start: 0.8443 (tt) cc_final: 0.8112 (tt) REVERT: B 1117 GLN cc_start: 0.8786 (tp40) cc_final: 0.8396 (tp-100) REVERT: C 176 PHE cc_start: 0.9014 (m-80) cc_final: 0.8809 (m-80) REVERT: C 180 ILE cc_start: 0.9216 (tp) cc_final: 0.9007 (tp) REVERT: C 181 TYR cc_start: 0.8008 (m-80) cc_final: 0.7798 (m-80) REVERT: C 291 TYR cc_start: 0.7239 (m-10) cc_final: 0.6652 (m-80) REVERT: C 563 TYR cc_start: 0.8785 (m-80) cc_final: 0.8504 (m-80) REVERT: C 644 MET cc_start: 0.7368 (ppp) cc_final: 0.6927 (ppp) REVERT: C 845 SER cc_start: 0.9398 (t) cc_final: 0.9124 (t) REVERT: C 939 MET cc_start: 0.8733 (mmp) cc_final: 0.8100 (mmm) REVERT: C 1040 GLU cc_start: 0.9368 (tp30) cc_final: 0.9147 (tp30) REVERT: C 1074 LEU cc_start: 0.8168 (tp) cc_final: 0.7799 (tt) REVERT: C 1117 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8533 (tp-100) REVERT: C 1220 PHE cc_start: 0.9110 (m-80) cc_final: 0.8711 (m-80) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1551 time to fit residues: 54.0231 Evaluate side-chains 143 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 178 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 152 optimal weight: 40.0000 chunk 346 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 316 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 207 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 HIS A1061 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.072490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.050109 restraints weight = 179328.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051585 restraints weight = 125172.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.052629 restraints weight = 98876.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053316 restraints weight = 84405.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053805 restraints weight = 75949.399| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31629 Z= 0.212 Angle : 0.772 16.261 43455 Z= 0.357 Chirality : 0.050 0.476 5547 Planarity : 0.004 0.064 5205 Dihedral : 4.268 19.415 3951 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.77 % 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: -0.96 (0.13), residues: 3666 helix: 0.36 (0.18), residues: 804 sheet: 0.14 (0.16), residues: 951 loop : -1.51 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 146 TYR 0.017 0.002 TYR B 413 PHE 0.047 0.002 PHE A 902 TRP 0.006 0.001 TRP A 168 HIS 0.008 0.002 HIS C1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (31386) covalent geometry : angle 0.69355 / 0.34 (42765) SS BOND : bond 0.00395 / 0.23 ( 39) SS BOND : angle 0.95363 / 0.72 ( 78) hydrogen bonds : bond 0.04708 / 3.36 ( 1099) hydrogen bonds : angle 5.85126 / 4.07 ( 3180) link_ALPHA1-3 : bond 0.00708 / 0.41 ( 24) link_ALPHA1-3 : angle 1.73606 / 1.32 ( 72) link_ALPHA1-6 : bond 0.00575 / 0.34 ( 21) link_ALPHA1-6 : angle 1.46528 / 1.09 ( 63) link_BETA1-4 : bond 0.01067 / 0.69 ( 84) link_BETA1-4 : angle 2.77606 / 1.93 ( 252) link_BETA1-6 : bond 0.00941 / 0.56 ( 12) link_BETA1-6 : angle 2.05181 / 1.35 ( 36) link_NAG-ASN : bond 0.00788 / 0.49 ( 63) link_NAG-ASN : angle 3.87143 / 2.87 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 176 PHE cc_start: 0.8893 (m-80) cc_final: 0.8631 (m-80) REVERT: A 181 TYR cc_start: 0.8102 (m-80) cc_final: 0.7896 (m-80) REVERT: A 644 MET cc_start: 0.7949 (ppp) cc_final: 0.7107 (ppp) REVERT: A 939 MET cc_start: 0.8598 (mmp) cc_final: 0.8257 (mmm) REVERT: A 1074 LEU cc_start: 0.8294 (tt) cc_final: 0.7996 (tt) REVERT: A 1117 GLN cc_start: 0.9051 (tp-100) cc_final: 0.8794 (tp-100) REVERT: A 1220 PHE cc_start: 0.9155 (m-80) cc_final: 0.8787 (m-80) REVERT: B 563 TYR cc_start: 0.8885 (m-80) cc_final: 0.8679 (m-80) REVERT: B 644 MET cc_start: 0.8021 (ppp) cc_final: 0.7438 (ppp) REVERT: B 939 MET cc_start: 0.8313 (mmp) cc_final: 0.7927 (mmm) REVERT: B 1074 LEU cc_start: 0.8518 (tt) cc_final: 0.8210 (tt) REVERT: B 1117 GLN cc_start: 0.8844 (tp40) cc_final: 0.8593 (tp40) REVERT: C 180 ILE cc_start: 0.9133 (tp) cc_final: 0.8894 (tp) REVERT: C 291 TYR cc_start: 0.7441 (m-10) cc_final: 0.7127 (m-80) REVERT: C 563 TYR cc_start: 0.8865 (m-80) cc_final: 0.8554 (m-80) REVERT: C 644 MET cc_start: 0.7653 (ppp) cc_final: 0.6965 (ppp) REVERT: C 782 ILE cc_start: 0.9268 (tt) cc_final: 0.8792 (mm) REVERT: C 939 MET cc_start: 0.8556 (mmp) cc_final: 0.8128 (mmm) REVERT: C 1074 LEU cc_start: 0.8228 (tp) cc_final: 0.7896 (tt) REVERT: C 1117 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8507 (tp-100) REVERT: C 1220 PHE cc_start: 0.9259 (m-80) cc_final: 0.8889 (m-80) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1487 time to fit residues: 46.8821 Evaluate side-chains 132 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 229 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 175 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 126 optimal weight: 0.0040 chunk 244 optimal weight: 20.0000 chunk 289 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 overall best weight: 3.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.072902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.050455 restraints weight = 184973.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.052013 restraints weight = 128205.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.053019 restraints weight = 100726.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053756 restraints weight = 86141.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.054244 restraints weight = 77698.490| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31629 Z= 0.163 Angle : 0.737 16.250 43455 Z= 0.334 Chirality : 0.049 0.494 5547 Planarity : 0.003 0.035 5205 Dihedral : 4.254 22.500 3951 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % 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: -0.97 (0.13), residues: 3666 helix: 0.41 (0.18), residues: 804 sheet: 0.14 (0.16), residues: 933 loop : -1.54 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 146 TYR 0.013 0.001 TYR B 291 PHE 0.045 0.001 PHE B 902 TRP 0.004 0.001 TRP A 168 HIS 0.005 0.001 HIS C1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (31386) covalent geometry : angle 0.65563 / 0.32 (42765) SS BOND : bond 0.00286 / 0.19 ( 39) SS BOND : angle 1.03557 / 0.78 ( 78) hydrogen bonds : bond 0.04446 / 3.19 ( 1099) hydrogen bonds : angle 5.69442 / 3.96 ( 3180) link_ALPHA1-3 : bond 0.00669 / 0.39 ( 24) link_ALPHA1-3 : angle 1.72320 / 1.31 ( 72) link_ALPHA1-6 : bond 0.00604 / 0.36 ( 21) link_ALPHA1-6 : angle 1.40121 / 1.04 ( 63) link_BETA1-4 : bond 0.01083 / 0.70 ( 84) link_BETA1-4 : angle 2.75301 / 1.92 ( 252) link_BETA1-6 : bond 0.00985 / 0.59 ( 12) link_BETA1-6 : angle 2.00776 / 1.32 ( 36) link_NAG-ASN : bond 0.00733 / 0.46 ( 63) link_NAG-ASN : angle 3.79032 / 2.81 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 176 PHE cc_start: 0.8923 (m-80) cc_final: 0.8648 (m-80) REVERT: A 181 TYR cc_start: 0.8111 (m-80) cc_final: 0.7899 (m-80) REVERT: A 291 TYR cc_start: 0.8054 (m-80) cc_final: 0.7227 (m-80) REVERT: A 471 LEU cc_start: 0.9494 (mt) cc_final: 0.9288 (pp) REVERT: A 644 MET cc_start: 0.7979 (ppp) cc_final: 0.7068 (ppp) REVERT: A 782 ILE cc_start: 0.9155 (tt) cc_final: 0.8770 (mm) REVERT: A 939 MET cc_start: 0.8409 (mmp) cc_final: 0.7987 (mmm) REVERT: A 1074 LEU cc_start: 0.8209 (tt) cc_final: 0.7940 (tt) REVERT: A 1220 PHE cc_start: 0.9174 (m-80) cc_final: 0.8761 (m-80) REVERT: B 91 PHE cc_start: 0.7682 (m-80) cc_final: 0.7002 (m-10) REVERT: B 291 TYR cc_start: 0.8089 (m-80) cc_final: 0.7174 (m-80) REVERT: B 563 TYR cc_start: 0.8865 (m-80) cc_final: 0.8556 (m-80) REVERT: B 644 MET cc_start: 0.8137 (ppp) cc_final: 0.7502 (ppp) REVERT: B 939 MET cc_start: 0.8371 (mmp) cc_final: 0.7888 (mmp) REVERT: B 1074 LEU cc_start: 0.8590 (tt) cc_final: 0.8355 (tt) REVERT: C 149 LEU cc_start: 0.9351 (tp) cc_final: 0.9125 (tp) REVERT: C 180 ILE cc_start: 0.9125 (tp) cc_final: 0.8877 (tp) REVERT: C 181 TYR cc_start: 0.7961 (m-80) cc_final: 0.7720 (m-80) REVERT: C 563 TYR cc_start: 0.8822 (m-80) cc_final: 0.8429 (m-80) REVERT: C 644 MET cc_start: 0.7869 (ppp) cc_final: 0.7116 (ppp) REVERT: C 939 MET cc_start: 0.8512 (mmp) cc_final: 0.8106 (mmm) REVERT: C 1074 LEU cc_start: 0.8326 (tp) cc_final: 0.7974 (tt) REVERT: C 1117 GLN cc_start: 0.8813 (tp-100) cc_final: 0.8418 (tp-100) REVERT: C 1220 PHE cc_start: 0.9279 (m-80) cc_final: 0.8872 (m-80) outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 0.1466 time to fit residues: 46.8329 Evaluate side-chains 141 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 71 optimal weight: 0.9990 chunk 237 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 324 optimal weight: 4.9990 chunk 347 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN A1117 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.072308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.050052 restraints weight = 177831.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.051590 restraints weight = 123182.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052636 restraints weight = 96532.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053353 restraints weight = 82120.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053816 restraints weight = 73691.778| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31629 Z= 0.158 Angle : 0.739 16.334 43455 Z= 0.335 Chirality : 0.049 0.492 5547 Planarity : 0.003 0.035 5205 Dihedral : 4.266 21.662 3951 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: -0.98 (0.13), residues: 3666 helix: 0.40 (0.18), residues: 807 sheet: 0.21 (0.16), residues: 933 loop : -1.59 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 490 TYR 0.011 0.001 TYR B 291 PHE 0.030 0.001 PHE B 902 TRP 0.006 0.001 TRP B 168 HIS 0.005 0.001 HIS A1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (31386) covalent geometry : angle 0.65929 / 0.32 (42765) SS BOND : bond 0.00320 / 0.20 ( 39) SS BOND : angle 0.94099 / 0.70 ( 78) hydrogen bonds : bond 0.04418 / 3.17 ( 1099) hydrogen bonds : angle 5.67129 / 3.95 ( 3180) link_ALPHA1-3 : bond 0.00667 / 0.39 ( 24) link_ALPHA1-3 : angle 1.72311 / 1.31 ( 72) link_ALPHA1-6 : bond 0.00592 / 0.35 ( 21) link_ALPHA1-6 : angle 1.42523 / 1.06 ( 63) link_BETA1-4 : bond 0.01090 / 0.70 ( 84) link_BETA1-4 : angle 2.75061 / 1.92 ( 252) link_BETA1-6 : bond 0.01017 / 0.61 ( 12) link_BETA1-6 : angle 2.01203 / 1.32 ( 36) link_NAG-ASN : bond 0.00725 / 0.45 ( 63) link_NAG-ASN : angle 3.78631 / 2.81 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.236 Fit side-chains REVERT: A 176 PHE cc_start: 0.8857 (m-80) cc_final: 0.8610 (m-80) REVERT: A 180 ILE cc_start: 0.9176 (tp) cc_final: 0.8946 (tp) REVERT: A 291 TYR cc_start: 0.7767 (m-80) cc_final: 0.6999 (m-80) REVERT: A 644 MET cc_start: 0.8020 (ppp) cc_final: 0.7040 (ppp) REVERT: A 782 ILE cc_start: 0.9061 (tt) cc_final: 0.8598 (mm) REVERT: A 939 MET cc_start: 0.8349 (mmp) cc_final: 0.7991 (mmm) REVERT: A 1074 LEU cc_start: 0.8217 (tt) cc_final: 0.7928 (tt) REVERT: A 1220 PHE cc_start: 0.9190 (m-80) cc_final: 0.8825 (m-80) REVERT: B 91 PHE cc_start: 0.7233 (m-80) cc_final: 0.6684 (m-10) REVERT: B 291 TYR cc_start: 0.8021 (m-80) cc_final: 0.7210 (m-80) REVERT: B 563 TYR cc_start: 0.8826 (m-80) cc_final: 0.8504 (m-80) REVERT: B 644 MET cc_start: 0.8218 (ppp) cc_final: 0.7515 (ppp) REVERT: B 1074 LEU cc_start: 0.8538 (tt) cc_final: 0.8277 (tt) REVERT: B 1117 GLN cc_start: 0.8839 (tp40) cc_final: 0.8576 (tp40) REVERT: C 180 ILE cc_start: 0.9114 (tp) cc_final: 0.8892 (tp) REVERT: C 563 TYR cc_start: 0.8803 (m-80) cc_final: 0.8461 (m-80) REVERT: C 644 MET cc_start: 0.7932 (ppp) cc_final: 0.7108 (ppp) REVERT: C 1074 LEU cc_start: 0.8405 (tp) cc_final: 0.8059 (tt) REVERT: C 1117 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8396 (tp-100) REVERT: C 1220 PHE cc_start: 0.9317 (m-80) cc_final: 0.8907 (m-80) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1694 time to fit residues: 54.8114 Evaluate side-chains 142 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 308 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 336 optimal weight: 10.0000 chunk 247 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 126 optimal weight: 0.0070 chunk 263 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.072863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.050520 restraints weight = 176921.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052075 restraints weight = 122230.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.053134 restraints weight = 95555.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053842 restraints weight = 81220.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.054322 restraints weight = 72939.456| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31629 Z= 0.133 Angle : 0.730 16.306 43455 Z= 0.326 Chirality : 0.050 0.500 5547 Planarity : 0.003 0.035 5205 Dihedral : 4.198 20.807 3951 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -0.92 (0.13), residues: 3666 helix: 0.50 (0.18), residues: 807 sheet: 0.22 (0.16), residues: 963 loop : -1.59 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 994 TYR 0.013 0.001 TYR B 291 PHE 0.023 0.001 PHE B 902 TRP 0.006 0.001 TRP B 189 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (31386) covalent geometry : angle 0.65111 / 0.31 (42765) SS BOND : bond 0.00271 / 0.17 ( 39) SS BOND : angle 1.03093 / 0.77 ( 78) hydrogen bonds : bond 0.04236 / 3.03 ( 1099) hydrogen bonds : angle 5.52631 / 3.86 ( 3180) link_ALPHA1-3 : bond 0.00661 / 0.38 ( 24) link_ALPHA1-3 : angle 1.70570 / 1.30 ( 72) link_ALPHA1-6 : bond 0.00600 / 0.35 ( 21) link_ALPHA1-6 : angle 1.38862 / 1.03 ( 63) link_BETA1-4 : bond 0.01091 / 0.71 ( 84) link_BETA1-4 : angle 2.73408 / 1.91 ( 252) link_BETA1-6 : bond 0.00995 / 0.59 ( 12) link_BETA1-6 : angle 1.94118 / 1.27 ( 36) link_NAG-ASN : bond 0.00713 / 0.45 ( 63) link_NAG-ASN : angle 3.72592 / 2.76 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.376 Fit side-chains REVERT: A 176 PHE cc_start: 0.8851 (m-80) cc_final: 0.8573 (m-80) REVERT: A 179 LYS cc_start: 0.9020 (ptmm) cc_final: 0.8716 (ptpp) REVERT: A 181 TYR cc_start: 0.8102 (m-10) cc_final: 0.7817 (m-10) REVERT: A 291 TYR cc_start: 0.7821 (m-80) cc_final: 0.7164 (m-80) REVERT: A 644 MET cc_start: 0.8027 (ppp) cc_final: 0.7028 (ppp) REVERT: A 782 ILE cc_start: 0.9036 (tt) cc_final: 0.8551 (mm) REVERT: A 1074 LEU cc_start: 0.8278 (tt) cc_final: 0.7980 (tt) REVERT: A 1117 GLN cc_start: 0.9076 (tp40) cc_final: 0.8739 (tp-100) REVERT: A 1220 PHE cc_start: 0.9167 (m-80) cc_final: 0.8778 (m-80) REVERT: B 91 PHE cc_start: 0.7250 (m-80) cc_final: 0.6411 (m-10) REVERT: B 291 TYR cc_start: 0.7923 (m-80) cc_final: 0.7396 (m-80) REVERT: B 563 TYR cc_start: 0.8822 (m-80) cc_final: 0.8506 (m-80) REVERT: B 644 MET cc_start: 0.8232 (ppp) cc_final: 0.7498 (ppp) REVERT: B 671 LEU cc_start: 0.9238 (pt) cc_final: 0.8715 (mm) REVERT: B 1074 LEU cc_start: 0.8588 (tt) cc_final: 0.8313 (tt) REVERT: B 1117 GLN cc_start: 0.8852 (tp40) cc_final: 0.8607 (tp-100) REVERT: C 179 LYS cc_start: 0.9249 (ptmm) cc_final: 0.8845 (ptmm) REVERT: C 181 TYR cc_start: 0.8301 (m-10) cc_final: 0.8094 (m-80) REVERT: C 291 TYR cc_start: 0.7305 (m-80) cc_final: 0.6500 (m-80) REVERT: C 563 TYR cc_start: 0.8778 (m-80) cc_final: 0.8426 (m-80) REVERT: C 644 MET cc_start: 0.7945 (ppp) cc_final: 0.7085 (ppp) REVERT: C 1074 LEU cc_start: 0.8381 (tp) cc_final: 0.8059 (tt) REVERT: C 1117 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8430 (tp-100) REVERT: C 1220 PHE cc_start: 0.9235 (m-80) cc_final: 0.8806 (m-80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1599 time to fit residues: 53.5138 Evaluate side-chains 143 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 146 optimal weight: 3.9990 chunk 300 optimal weight: 40.0000 chunk 359 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 355 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 HIS ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 GLN A1061 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.071554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.049407 restraints weight = 178396.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.050916 restraints weight = 123574.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.051946 restraints weight = 96836.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.052665 restraints weight = 82165.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053078 restraints weight = 73686.117| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31629 Z= 0.176 Angle : 0.760 16.270 43455 Z= 0.346 Chirality : 0.050 0.491 5547 Planarity : 0.003 0.038 5205 Dihedral : 4.389 21.875 3951 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -1.07 (0.13), residues: 3666 helix: 0.41 (0.18), residues: 807 sheet: 0.04 (0.16), residues: 963 loop : -1.65 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1235 TYR 0.021 0.001 TYR B 800 PHE 0.025 0.002 PHE B 902 TRP 0.006 0.001 TRP B 168 HIS 0.006 0.001 HIS A1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (31386) covalent geometry : angle 0.68168 / 0.33 (42765) SS BOND : bond 0.00319 / 0.21 ( 39) SS BOND : angle 0.98181 / 0.74 ( 78) hydrogen bonds : bond 0.04463 / 3.19 ( 1099) hydrogen bonds : angle 5.62994 / 3.93 ( 3180) link_ALPHA1-3 : bond 0.00676 / 0.39 ( 24) link_ALPHA1-3 : angle 1.73583 / 1.33 ( 72) link_ALPHA1-6 : bond 0.00591 / 0.35 ( 21) link_ALPHA1-6 : angle 1.46262 / 1.09 ( 63) link_BETA1-4 : bond 0.01098 / 0.71 ( 84) link_BETA1-4 : angle 2.76048 / 1.92 ( 252) link_BETA1-6 : bond 0.01023 / 0.61 ( 12) link_BETA1-6 : angle 2.01294 / 1.32 ( 36) link_NAG-ASN : bond 0.00767 / 0.48 ( 63) link_NAG-ASN : angle 3.80259 / 2.81 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.229 Fit side-chains REVERT: A 91 PHE cc_start: 0.7585 (m-80) cc_final: 0.6593 (m-80) REVERT: A 108 TYR cc_start: 0.8607 (m-80) cc_final: 0.7963 (m-80) REVERT: A 176 PHE cc_start: 0.8798 (m-80) cc_final: 0.8501 (m-80) REVERT: A 291 TYR cc_start: 0.7915 (m-80) cc_final: 0.7411 (m-80) REVERT: A 644 MET cc_start: 0.8116 (ppp) cc_final: 0.7119 (ppp) REVERT: A 790 MET cc_start: 0.9231 (mmm) cc_final: 0.8709 (mmm) REVERT: A 939 MET cc_start: 0.8540 (mmp) cc_final: 0.8065 (mmm) REVERT: A 1074 LEU cc_start: 0.8195 (tt) cc_final: 0.7929 (tt) REVERT: A 1117 GLN cc_start: 0.9062 (tp40) cc_final: 0.8754 (tp-100) REVERT: A 1220 PHE cc_start: 0.9264 (m-80) cc_final: 0.8878 (m-80) REVERT: B 91 PHE cc_start: 0.7369 (m-80) cc_final: 0.6478 (m-10) REVERT: B 291 TYR cc_start: 0.8113 (m-80) cc_final: 0.7679 (m-80) REVERT: B 563 TYR cc_start: 0.8900 (m-80) cc_final: 0.8599 (m-80) REVERT: B 644 MET cc_start: 0.8201 (ppp) cc_final: 0.7384 (ppp) REVERT: B 844 GLU cc_start: 0.8839 (pp20) cc_final: 0.8622 (pp20) REVERT: B 1074 LEU cc_start: 0.8592 (tt) cc_final: 0.8312 (tt) REVERT: B 1102 LEU cc_start: 0.9647 (pp) cc_final: 0.9304 (mp) REVERT: C 180 ILE cc_start: 0.9175 (tp) cc_final: 0.8962 (tp) REVERT: C 181 TYR cc_start: 0.8400 (m-10) cc_final: 0.8065 (m-80) REVERT: C 563 TYR cc_start: 0.8820 (m-80) cc_final: 0.8446 (m-80) REVERT: C 644 MET cc_start: 0.8098 (ppp) cc_final: 0.7245 (ppp) REVERT: C 658 LYS cc_start: 0.9251 (ptpt) cc_final: 0.8826 (pttt) REVERT: C 939 MET cc_start: 0.7574 (mpp) cc_final: 0.7140 (mpp) REVERT: C 1117 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8554 (tp-100) REVERT: C 1220 PHE cc_start: 0.9300 (m-80) cc_final: 0.8868 (m-80) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1575 time to fit residues: 52.3480 Evaluate side-chains 141 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 158 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 355 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 346 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 0.0770 chunk 58 optimal weight: 0.2980 chunk 188 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 362 optimal weight: 10.0000 overall best weight: 2.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.072222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049997 restraints weight = 176625.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.051532 restraints weight = 122001.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052597 restraints weight = 95418.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053311 restraints weight = 80885.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.053800 restraints weight = 72494.752| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31629 Z= 0.138 Angle : 0.745 16.223 43455 Z= 0.333 Chirality : 0.050 0.502 5547 Planarity : 0.003 0.037 5205 Dihedral : 4.278 22.235 3951 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -1.03 (0.13), residues: 3666 helix: 0.44 (0.18), residues: 807 sheet: 0.13 (0.16), residues: 924 loop : -1.63 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1235 TYR 0.015 0.001 TYR B 291 PHE 0.019 0.001 PHE A 902 TRP 0.009 0.001 TRP B 189 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (31386) covalent geometry : angle 0.66679 / 0.32 (42765) SS BOND : bond 0.00278 / 0.18 ( 39) SS BOND : angle 0.96555 / 0.71 ( 78) hydrogen bonds : bond 0.04303 / 3.08 ( 1099) hydrogen bonds : angle 5.49887 / 3.84 ( 3180) link_ALPHA1-3 : bond 0.00651 / 0.38 ( 24) link_ALPHA1-3 : angle 1.71457 / 1.30 ( 72) link_ALPHA1-6 : bond 0.00608 / 0.35 ( 21) link_ALPHA1-6 : angle 1.40029 / 1.04 ( 63) link_BETA1-4 : bond 0.01086 / 0.71 ( 84) link_BETA1-4 : angle 2.74162 / 1.91 ( 252) link_BETA1-6 : bond 0.00972 / 0.58 ( 12) link_BETA1-6 : angle 1.93582 / 1.27 ( 36) link_NAG-ASN : bond 0.00679 / 0.42 ( 63) link_NAG-ASN : angle 3.77193 / 2.81 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.179 Fit side-chains REVERT: A 91 PHE cc_start: 0.7548 (m-80) cc_final: 0.6582 (m-80) REVERT: A 108 TYR cc_start: 0.8587 (m-80) cc_final: 0.7955 (m-80) REVERT: A 176 PHE cc_start: 0.8842 (m-80) cc_final: 0.8551 (m-80) REVERT: A 181 TYR cc_start: 0.8316 (m-80) cc_final: 0.8001 (m-80) REVERT: A 291 TYR cc_start: 0.7935 (m-80) cc_final: 0.7419 (m-80) REVERT: A 644 MET cc_start: 0.8111 (ppp) cc_final: 0.7053 (ppp) REVERT: A 782 ILE cc_start: 0.9052 (tt) cc_final: 0.8502 (mm) REVERT: A 939 MET cc_start: 0.8563 (mmp) cc_final: 0.8113 (mmm) REVERT: A 1074 LEU cc_start: 0.8167 (tt) cc_final: 0.7880 (tt) REVERT: A 1117 GLN cc_start: 0.9042 (tp40) cc_final: 0.8702 (tp-100) REVERT: A 1209 MET cc_start: 0.8709 (mmp) cc_final: 0.8224 (mmm) REVERT: A 1220 PHE cc_start: 0.9249 (m-80) cc_final: 0.8860 (m-80) REVERT: B 91 PHE cc_start: 0.7337 (m-80) cc_final: 0.6468 (m-10) REVERT: B 291 TYR cc_start: 0.8078 (m-80) cc_final: 0.7645 (m-80) REVERT: B 563 TYR cc_start: 0.8867 (m-80) cc_final: 0.8568 (m-80) REVERT: B 644 MET cc_start: 0.8186 (ppp) cc_final: 0.7364 (ppp) REVERT: B 819 CYS cc_start: 0.9056 (m) cc_final: 0.7968 (t) REVERT: B 1074 LEU cc_start: 0.8567 (tt) cc_final: 0.8275 (tt) REVERT: B 1102 LEU cc_start: 0.9620 (pp) cc_final: 0.9376 (mp) REVERT: C 179 LYS cc_start: 0.9195 (ptmm) cc_final: 0.8639 (ptmm) REVERT: C 563 TYR cc_start: 0.8781 (m-80) cc_final: 0.8412 (m-80) REVERT: C 644 MET cc_start: 0.8099 (ppp) cc_final: 0.7247 (ppp) REVERT: C 658 LYS cc_start: 0.9273 (ptpt) cc_final: 0.8820 (pttt) REVERT: C 1074 LEU cc_start: 0.8398 (tp) cc_final: 0.8043 (tt) REVERT: C 1117 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8508 (tp-100) REVERT: C 1220 PHE cc_start: 0.9291 (m-80) cc_final: 0.8823 (m-80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1620 time to fit residues: 53.8420 Evaluate side-chains 148 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 206 optimal weight: 7.9990 chunk 353 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 287 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN A1095 ASN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN B1095 ASN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN C1061 GLN C1095 ASN ** C1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.073058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.050782 restraints weight = 174504.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052346 restraints weight = 120043.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053425 restraints weight = 93759.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.054172 restraints weight = 79412.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054648 restraints weight = 70932.904| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31629 Z= 0.122 Angle : 0.739 16.341 43455 Z= 0.327 Chirality : 0.050 0.507 5547 Planarity : 0.003 0.036 5205 Dihedral : 4.171 28.853 3951 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.89 (0.13), residues: 3666 helix: 0.56 (0.18), residues: 804 sheet: 0.31 (0.17), residues: 945 loop : -1.62 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1235 TYR 0.020 0.001 TYR C 800 PHE 0.015 0.001 PHE B 896 TRP 0.009 0.001 TRP B 189 HIS 0.002 0.001 HIS A1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (31386) covalent geometry : angle 0.66219 / 0.31 (42765) SS BOND : bond 0.00245 / 0.16 ( 39) SS BOND : angle 0.96195 / 0.71 ( 78) hydrogen bonds : bond 0.04080 / 2.91 ( 1099) hydrogen bonds : angle 5.32443 / 3.71 ( 3180) link_ALPHA1-3 : bond 0.00658 / 0.38 ( 24) link_ALPHA1-3 : angle 1.68241 / 1.28 ( 72) link_ALPHA1-6 : bond 0.00603 / 0.35 ( 21) link_ALPHA1-6 : angle 1.36202 / 1.00 ( 63) link_BETA1-4 : bond 0.01106 / 0.72 ( 84) link_BETA1-4 : angle 2.73027 / 1.90 ( 252) link_BETA1-6 : bond 0.00978 / 0.58 ( 12) link_BETA1-6 : angle 1.82585 / 1.20 ( 36) link_NAG-ASN : bond 0.00682 / 0.43 ( 63) link_NAG-ASN : angle 3.70955 / 2.76 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.165 Fit side-chains REVERT: A 91 PHE cc_start: 0.7535 (m-80) cc_final: 0.6570 (m-80) REVERT: A 108 TYR cc_start: 0.8556 (m-80) cc_final: 0.7922 (m-80) REVERT: A 176 PHE cc_start: 0.8745 (m-80) cc_final: 0.8485 (m-80) REVERT: A 181 TYR cc_start: 0.8146 (m-80) cc_final: 0.7875 (m-80) REVERT: A 291 TYR cc_start: 0.7918 (m-80) cc_final: 0.7478 (m-80) REVERT: A 644 MET cc_start: 0.8113 (ppp) cc_final: 0.7051 (ppp) REVERT: A 782 ILE cc_start: 0.8946 (tt) cc_final: 0.8435 (mm) REVERT: A 939 MET cc_start: 0.8521 (mmp) cc_final: 0.8105 (mmm) REVERT: A 1074 LEU cc_start: 0.8398 (tt) cc_final: 0.8094 (tt) REVERT: A 1117 GLN cc_start: 0.9085 (tp40) cc_final: 0.8765 (tp-100) REVERT: A 1209 MET cc_start: 0.8720 (mmp) cc_final: 0.8216 (mmm) REVERT: A 1220 PHE cc_start: 0.9215 (m-80) cc_final: 0.8811 (m-80) REVERT: B 91 PHE cc_start: 0.7355 (m-80) cc_final: 0.6531 (m-10) REVERT: B 291 TYR cc_start: 0.7963 (m-80) cc_final: 0.7594 (m-80) REVERT: B 563 TYR cc_start: 0.8855 (m-80) cc_final: 0.8546 (m-80) REVERT: B 644 MET cc_start: 0.8234 (ppp) cc_final: 0.7460 (ppp) REVERT: B 658 LYS cc_start: 0.9225 (ptpt) cc_final: 0.8871 (pttt) REVERT: B 671 LEU cc_start: 0.9229 (pt) cc_final: 0.8745 (mm) REVERT: B 819 CYS cc_start: 0.9038 (m) cc_final: 0.8001 (t) REVERT: B 1074 LEU cc_start: 0.8546 (tt) cc_final: 0.8244 (tt) REVERT: B 1102 LEU cc_start: 0.9627 (pp) cc_final: 0.9326 (mp) REVERT: C 181 TYR cc_start: 0.8306 (m-80) cc_final: 0.7902 (m-80) REVERT: C 563 TYR cc_start: 0.8721 (m-80) cc_final: 0.8348 (m-80) REVERT: C 644 MET cc_start: 0.8059 (ppp) cc_final: 0.7266 (ppp) REVERT: C 658 LYS cc_start: 0.9251 (ptpt) cc_final: 0.8784 (pttt) REVERT: C 782 ILE cc_start: 0.9034 (tt) cc_final: 0.8552 (mm) REVERT: C 819 CYS cc_start: 0.8856 (m) cc_final: 0.8236 (t) REVERT: C 1074 LEU cc_start: 0.8206 (tp) cc_final: 0.7870 (tt) REVERT: C 1117 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8446 (tp40) REVERT: C 1220 PHE cc_start: 0.9240 (m-80) cc_final: 0.8763 (m-80) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1623 time to fit residues: 55.9431 Evaluate side-chains 155 residues out of total 3147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.9364 > 50: distance: 39 - 40: 3.159 distance: 40 - 41: 9.104 distance: 40 - 43: 5.054 distance: 41 - 42: 3.317 distance: 41 - 50: 5.659 distance: 43 - 44: 4.920 distance: 44 - 45: 10.948 distance: 45 - 46: 9.333 distance: 46 - 47: 4.759 distance: 47 - 49: 7.781 distance: 50 - 51: 11.106 distance: 50 - 167: 10.539 distance: 51 - 52: 9.680 distance: 51 - 54: 7.438 distance: 52 - 53: 6.496 distance: 52 - 61: 8.109 distance: 53 - 164: 11.863 distance: 54 - 55: 10.109 distance: 55 - 56: 7.117 distance: 55 - 57: 6.493 distance: 56 - 58: 6.522 distance: 57 - 59: 7.376 distance: 58 - 60: 6.467 distance: 59 - 60: 5.743 distance: 61 - 62: 6.006 distance: 62 - 63: 12.457 distance: 62 - 65: 14.034 distance: 63 - 64: 7.951 distance: 63 - 69: 12.271 distance: 64 - 204: 16.240 distance: 65 - 66: 20.108 distance: 66 - 67: 7.283 distance: 66 - 68: 9.328 distance: 69 - 70: 13.265 distance: 70 - 71: 20.629 distance: 70 - 73: 8.673 distance: 71 - 72: 49.102 distance: 71 - 77: 23.969 distance: 73 - 74: 13.543 distance: 73 - 75: 14.605 distance: 74 - 76: 9.292 distance: 77 - 78: 6.007 distance: 78 - 79: 11.897 distance: 78 - 81: 9.475 distance: 79 - 80: 25.037 distance: 79 - 85: 16.385 distance: 81 - 82: 23.119 distance: 82 - 83: 15.484 distance: 82 - 84: 26.431 distance: 84 - 231: 9.186 distance: 85 - 86: 14.621 distance: 86 - 87: 5.905 distance: 86 - 89: 19.915 distance: 87 - 88: 6.216 distance: 87 - 93: 9.385 distance: 89 - 90: 14.420 distance: 90 - 91: 6.541 distance: 90 - 92: 7.744 distance: 93 - 94: 8.469 distance: 94 - 95: 14.515 distance: 94 - 97: 6.426 distance: 95 - 96: 7.159 distance: 95 - 100: 12.141 distance: 96 - 121: 24.267 distance: 97 - 98: 11.636 distance: 97 - 99: 16.686 distance: 100 - 101: 11.434 distance: 101 - 102: 10.568 distance: 101 - 104: 15.759 distance: 102 - 103: 11.824 distance: 102 - 106: 4.643 distance: 103 - 129: 19.874 distance: 104 - 105: 12.236 distance: 106 - 107: 6.207 distance: 107 - 108: 11.374 distance: 108 - 109: 11.306 distance: 108 - 113: 10.433 distance: 109 - 134: 12.467 distance: 110 - 111: 9.559 distance: 110 - 112: 3.720 distance: 113 - 114: 5.696 distance: 114 - 115: 6.448 distance: 114 - 117: 4.105 distance: 115 - 116: 13.542 distance: 115 - 121: 6.094 distance: 117 - 118: 3.767 distance: 117 - 119: 13.256