Starting phenix.real_space_refine on Tue Apr 7 13:01:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lvs_63424/04_2026/9lvs_63424_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lvs_63424/04_2026/9lvs_63424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lvs_63424/04_2026/9lvs_63424_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lvs_63424/04_2026/9lvs_63424_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lvs_63424/04_2026/9lvs_63424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lvs_63424/04_2026/9lvs_63424.map" } resolution = 2.95 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= 0.027 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: 5 Type Number sf(0) Gaussians S 126 5.16 5 Cl 6 4.86 5 C 17400 2.51 5 N 4455 2.21 5 O 5436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27423 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8657 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 2 Chain: "B" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8657 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 2 Chain: "C" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8657 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'EZO': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'EZO': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'EZO': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.06, per 1000 atoms: 0.15 Number of scatterers: 27423 At special positions: 0 Unit cell: (156.04, 146.08, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 6 17.00 S 126 16.00 O 5436 8.00 N 4455 7.00 C 17400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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=5, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B1301 " - " ASN B 331 " " NAG D 1 " - " ASN A 61 " " NAG G 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 122 " " NAG O 1 " - " ASN A 282 " " NAG Q 1 " - " ASN A 17 " " NAG S 1 " - " ASN B 61 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 343 " " NAG V 1 " - " ASN B 709 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1074 " " NAG Z 1 " - " ASN B1098 " " NAG b 1 " - " ASN B 122 " " NAG d 1 " - " ASN B 282 " " NAG f 1 " - " ASN B 17 " " NAG g 1 " - " ASN B 149 " " NAG i 1 " - " ASN C 616 " " NAG n 1 " - " ASN C1074 " " NAG p 1 " - " ASN C1134 " " NAG q 1 " - " ASN C 122 " " NAG s 1 " - " ASN C 282 " " NAG u 1 " - " ASN C 17 " " NAG v 1 " - " ASN C 149 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 710.4 milliseconds 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6210 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 51 sheets defined 24.6% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.504A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.539A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.949A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.224A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 837 through 841 removed outlier: 3.621A pdb=" N LEU A 841 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.387A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.543A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.309A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.919A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.527A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.523A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.885A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.809A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.937A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.103A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.805A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.319A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.220A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.523A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.678A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.705A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.881A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 843 through 848 removed outlier: 3.671A pdb=" N ARG C 847 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.115A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.723A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.991A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.867A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.891A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.891A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.056A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.618A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.830A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.607A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.250A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.536A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.648A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.132A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.051A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.051A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.228A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.479A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 713 through 728 removed outlier: 6.587A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.802A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.996A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.996A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.355A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.005A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.587A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.750A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.482A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.146A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.343A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.999A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.999A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.190A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.719A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.536A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.112A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU C 226 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.112A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.022A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 152 through 156 removed outlier: 6.332A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.701A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.166A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.166A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.147A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.830A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.965A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1081 through 1083 1090 hydrogen bonds defined for protein. 2982 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: 6.21 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5673 1.33 - 1.46: 8805 1.46 - 1.59: 13395 1.59 - 1.72: 12 1.72 - 1.84: 156 Bond restraints: 28041 Sorted by residual: bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.518 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CA ASN A 234 " pdb=" C ASN A 234 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.19e-02 7.06e+03 2.83e+01 bond pdb=" C ASN A 234 " pdb=" N ILE A 235 " ideal model delta sigma weight residual 1.331 1.263 0.067 1.29e-02 6.01e+03 2.73e+01 bond pdb=" N ASN C 234 " pdb=" CA ASN C 234 " ideal model delta sigma weight residual 1.454 1.394 0.060 1.18e-02 7.18e+03 2.58e+01 bond pdb=" C15 EZO A1302 " pdb=" N14 EZO A1302 " ideal model delta sigma weight residual 1.361 1.447 -0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 28036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 37595 2.57 - 5.14: 505 5.14 - 7.71: 54 7.71 - 10.28: 9 10.28 - 12.85: 3 Bond angle restraints: 38166 Sorted by residual: angle pdb=" N ASN B 165 " pdb=" CA ASN B 165 " pdb=" C ASN B 165 " ideal model delta sigma weight residual 111.02 123.87 -12.85 1.25e+00 6.40e-01 1.06e+02 angle pdb=" N CYS B 166 " pdb=" CA CYS B 166 " pdb=" C CYS B 166 " ideal model delta sigma weight residual 108.23 120.95 -12.72 1.72e+00 3.38e-01 5.47e+01 angle pdb=" C ILE C 233 " pdb=" CA ILE C 233 " pdb=" CB ILE C 233 " ideal model delta sigma weight residual 111.13 102.63 8.50 1.27e+00 6.20e-01 4.48e+01 angle pdb=" N ASN C 234 " pdb=" CA ASN C 234 " pdb=" CB ASN C 234 " ideal model delta sigma weight residual 110.85 101.43 9.42 1.54e+00 4.22e-01 3.74e+01 angle pdb=" C ASN B 165 " pdb=" CA ASN B 165 " pdb=" CB ASN B 165 " ideal model delta sigma weight residual 112.30 101.58 10.72 1.84e+00 2.95e-01 3.39e+01 ... (remaining 38161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.27: 16280 25.27 - 50.53: 1225 50.53 - 75.80: 232 75.80 - 101.06: 60 101.06 - 126.33: 35 Dihedral angle restraints: 17832 sinusoidal: 8157 harmonic: 9675 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -4.44 -81.56 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 13.37 79.63 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -152.01 66.01 1 1.00e+01 1.00e-02 5.70e+01 ... (remaining 17829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 4517 0.175 - 0.350: 13 0.350 - 0.525: 2 0.525 - 0.700: 0 0.700 - 0.875: 1 Chirality restraints: 4533 Sorted by residual: chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.12e+02 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 4530 not shown) Planarity restraints: 4866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " -0.017 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" CG ASN B 165 " 0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " -0.021 2.00e-02 2.50e+03 2.03e-02 5.17e+00 pdb=" CG ASN B1074 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " -0.020 2.00e-02 2.50e+03 1.92e-02 4.61e+00 pdb=" CG ASN C1074 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG n 1 " -0.022 2.00e-02 2.50e+03 ... (remaining 4863 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3033 2.75 - 3.29: 26393 3.29 - 3.82: 46142 3.82 - 4.36: 55646 4.36 - 4.90: 96780 Nonbonded interactions: 227994 Sorted by model distance: nonbonded pdb=" O ASN A 978 " pdb=" OG SER A 982 " model vdw 2.212 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.226 3.040 nonbonded pdb=" OE1 GLU C 406 " pdb=" OH TYR C 495 " model vdw 2.236 3.040 nonbonded pdb=" CZ PHE A 377 " pdb=" C27 EZO A1303 " model vdw 2.237 3.760 nonbonded pdb=" O ASP C 80 " pdb=" OH TYR C 265 " model vdw 2.238 3.040 ... (remaining 227989 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.570 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.007 0.821 28166 Z= 0.564 Angle : 0.763 21.618 38481 Z= 0.385 Chirality : 0.050 0.875 4533 Planarity : 0.004 0.052 4836 Dihedral : 18.681 126.330 11487 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 0.52 % Allowed : 24.62 % Favored : 74.86 % 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: -0.77 (0.14), residues: 3309 helix: 1.31 (0.20), residues: 696 sheet: -0.18 (0.19), residues: 723 loop : -1.39 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 355 TYR 0.021 0.001 TYR B1138 PHE 0.029 0.001 PHE C 823 TRP 0.010 0.001 TRP C 152 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00510 (28041) covalent geometry : angle 0.70689 (38166) SS BOND : bond 0.00342 ( 45) SS BOND : angle 1.19782 ( 90) hydrogen bonds : bond 0.12187 ( 1050) hydrogen bonds : angle 6.83369 ( 2982) Misc. bond : bond 0.36726 ( 5) link_BETA1-4 : bond 0.00412 ( 45) link_BETA1-4 : angle 2.34015 ( 135) link_NAG-ASN : bond 0.00914 ( 30) link_NAG-ASN : angle 5.20330 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7781 (tm-30) REVERT: C 1045 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8464 (tttp) outliers start: 15 outliers final: 1 residues processed: 233 average time/residue: 0.6185 time to fit residues: 169.1115 Evaluate side-chains 190 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 234 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN B 30 ASN B 474 GLN B 603 ASN C 234 ASN C 343 ASN C 544 ASN C 675 GLN C 710 ASN C1101 HIS C1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.107588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.079093 restraints weight = 41455.771| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.53 r_work: 0.2785 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28166 Z= 0.159 Angle : 0.642 20.396 38481 Z= 0.303 Chirality : 0.046 0.585 4533 Planarity : 0.004 0.043 4836 Dihedral : 12.205 119.664 5570 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 2.63 % Allowed : 22.79 % Favored : 74.59 % 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: -0.58 (0.14), residues: 3309 helix: 1.38 (0.20), residues: 732 sheet: -0.01 (0.19), residues: 708 loop : -1.31 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.023 0.001 TYR B1138 PHE 0.013 0.001 PHE A 377 TRP 0.009 0.001 TRP C 152 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00375 (28041) covalent geometry : angle 0.58567 (38166) SS BOND : bond 0.00352 ( 45) SS BOND : angle 1.35621 ( 90) hydrogen bonds : bond 0.04140 ( 1050) hydrogen bonds : angle 5.53912 ( 2982) Misc. bond : bond 0.00222 ( 5) link_BETA1-4 : bond 0.00411 ( 45) link_BETA1-4 : angle 1.85614 ( 135) link_NAG-ASN : bond 0.00852 ( 30) link_NAG-ASN : angle 4.86509 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 206 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: C 780 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8231 (mt-10) REVERT: C 1050 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8799 (ptm) outliers start: 76 outliers final: 19 residues processed: 264 average time/residue: 0.5242 time to fit residues: 167.0930 Evaluate side-chains 202 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 190 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 328 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN B 207 HIS B 474 GLN B 603 ASN C 30 ASN C 544 ASN C 675 GLN C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.079788 restraints weight = 41434.784| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.53 r_work: 0.2800 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28166 Z= 0.122 Angle : 0.604 20.182 38481 Z= 0.284 Chirality : 0.045 0.538 4533 Planarity : 0.003 0.042 4836 Dihedral : 10.328 117.493 5568 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 2.77 % Allowed : 22.79 % Favored : 74.45 % 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: -0.45 (0.14), residues: 3309 helix: 1.54 (0.20), residues: 732 sheet: 0.08 (0.19), residues: 729 loop : -1.27 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.018 0.001 TYR B1067 PHE 0.023 0.001 PHE C 823 TRP 0.007 0.001 TRP C 152 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00279 (28041) covalent geometry : angle 0.54876 (38166) SS BOND : bond 0.00278 ( 45) SS BOND : angle 1.14425 ( 90) hydrogen bonds : bond 0.03810 ( 1050) hydrogen bonds : angle 5.27541 ( 2982) Misc. bond : bond 0.00059 ( 5) link_BETA1-4 : bond 0.00399 ( 45) link_BETA1-4 : angle 1.84606 ( 135) link_NAG-ASN : bond 0.00845 ( 30) link_NAG-ASN : angle 4.69112 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 211 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7759 (tm-30) REVERT: A 190 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8362 (mtt-85) REVERT: B 180 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: B 787 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8111 (mm-40) REVERT: C 111 ASP cc_start: 0.8544 (m-30) cc_final: 0.8336 (t0) REVERT: C 1050 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8684 (ptm) outliers start: 80 outliers final: 31 residues processed: 275 average time/residue: 0.4952 time to fit residues: 164.4229 Evaluate side-chains 225 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 56 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 238 optimal weight: 0.8980 chunk 283 optimal weight: 0.0030 chunk 187 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 657 ASN B 474 GLN B 603 ASN B 901 GLN B 914 ASN C 493 GLN C 675 GLN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.077270 restraints weight = 41513.321| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.53 r_work: 0.2753 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28166 Z= 0.219 Angle : 0.650 19.874 38481 Z= 0.308 Chirality : 0.047 0.544 4533 Planarity : 0.004 0.047 4836 Dihedral : 9.443 115.961 5568 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 3.18 % Allowed : 22.72 % Favored : 74.10 % 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: -0.52 (0.14), residues: 3309 helix: 1.43 (0.20), residues: 732 sheet: 0.06 (0.19), residues: 729 loop : -1.29 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 78 TYR 0.025 0.001 TYR B1138 PHE 0.026 0.001 PHE C 823 TRP 0.008 0.001 TRP C 152 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00528 (28041) covalent geometry : angle 0.59566 (38166) SS BOND : bond 0.00405 ( 45) SS BOND : angle 1.50095 ( 90) hydrogen bonds : bond 0.04258 ( 1050) hydrogen bonds : angle 5.31520 ( 2982) Misc. bond : bond 0.00107 ( 5) link_BETA1-4 : bond 0.00360 ( 45) link_BETA1-4 : angle 1.89702 ( 135) link_NAG-ASN : bond 0.00812 ( 30) link_NAG-ASN : angle 4.72437 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 188 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: B 787 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7971 (mm-40) REVERT: C 78 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.6935 (mmm160) REVERT: C 111 ASP cc_start: 0.8583 (m-30) cc_final: 0.8328 (t0) REVERT: C 617 CYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8241 (m) REVERT: C 1050 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8822 (ptm) outliers start: 92 outliers final: 41 residues processed: 263 average time/residue: 0.5083 time to fit residues: 161.1067 Evaluate side-chains 219 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 205 optimal weight: 0.6980 chunk 246 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 240 optimal weight: 0.0870 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 308 optimal weight: 4.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 914 ASN B 474 GLN B 603 ASN B 901 GLN C 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.078162 restraints weight = 41415.992| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.52 r_work: 0.2766 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28166 Z= 0.167 Angle : 0.622 19.789 38481 Z= 0.293 Chirality : 0.046 0.513 4533 Planarity : 0.003 0.045 4836 Dihedral : 8.839 115.289 5568 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 3.11 % Allowed : 23.06 % Favored : 73.82 % 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: -0.47 (0.14), residues: 3309 helix: 1.49 (0.20), residues: 732 sheet: 0.04 (0.19), residues: 708 loop : -1.23 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.018 0.001 TYR A1067 PHE 0.026 0.001 PHE C 823 TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00397 (28041) covalent geometry : angle 0.56606 (38166) SS BOND : bond 0.00377 ( 45) SS BOND : angle 1.39160 ( 90) hydrogen bonds : bond 0.03970 ( 1050) hydrogen bonds : angle 5.23618 ( 2982) Misc. bond : bond 0.00083 ( 5) link_BETA1-4 : bond 0.00383 ( 45) link_BETA1-4 : angle 1.94680 ( 135) link_NAG-ASN : bond 0.00813 ( 30) link_NAG-ASN : angle 4.67711 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 194 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 GLU cc_start: 0.7674 (pm20) cc_final: 0.7412 (pm20) REVERT: B 180 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: B 787 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7884 (mm-40) REVERT: B 902 MET cc_start: 0.8908 (tpp) cc_final: 0.8673 (mmm) REVERT: B 919 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8540 (p0) REVERT: C 78 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.6918 (mmm160) REVERT: C 111 ASP cc_start: 0.8572 (m-30) cc_final: 0.8293 (t0) REVERT: C 1050 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8738 (ptm) outliers start: 90 outliers final: 45 residues processed: 268 average time/residue: 0.5052 time to fit residues: 163.6015 Evaluate side-chains 230 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 130 optimal weight: 0.0030 chunk 103 optimal weight: 2.9990 chunk 164 optimal weight: 0.3980 chunk 126 optimal weight: 0.0270 chunk 234 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.2852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN B 207 HIS B 474 GLN B 603 ASN C 675 GLN C1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.079554 restraints weight = 41349.173| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.51 r_work: 0.2775 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28166 Z= 0.129 Angle : 0.606 19.779 38481 Z= 0.284 Chirality : 0.045 0.494 4533 Planarity : 0.003 0.043 4836 Dihedral : 8.164 114.424 5568 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 2.94 % Allowed : 23.06 % Favored : 74.00 % 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: -0.41 (0.14), residues: 3309 helix: 1.59 (0.20), residues: 732 sheet: 0.07 (0.19), residues: 720 loop : -1.22 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.026 0.001 TYR B1138 PHE 0.028 0.001 PHE C 823 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00301 (28041) covalent geometry : angle 0.55018 (38166) SS BOND : bond 0.00284 ( 45) SS BOND : angle 1.24068 ( 90) hydrogen bonds : bond 0.03728 ( 1050) hydrogen bonds : angle 5.09951 ( 2982) Misc. bond : bond 0.00067 ( 5) link_BETA1-4 : bond 0.00395 ( 45) link_BETA1-4 : angle 2.00824 ( 135) link_NAG-ASN : bond 0.00816 ( 30) link_NAG-ASN : angle 4.61567 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 201 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8651 (mtt-85) cc_final: 0.8434 (mtt-85) REVERT: A 646 ARG cc_start: 0.8842 (ttp80) cc_final: 0.8575 (mtp85) REVERT: A 1019 ARG cc_start: 0.8660 (tpt170) cc_final: 0.8449 (tpt170) REVERT: B 96 GLU cc_start: 0.7720 (pm20) cc_final: 0.7498 (pm20) REVERT: B 180 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: B 787 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7842 (mm-40) REVERT: C 78 ARG cc_start: 0.7447 (mmm-85) cc_final: 0.6942 (mmm160) REVERT: C 755 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6325 (mp10) REVERT: C 1050 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8902 (ptm) REVERT: C 1098 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8053 (p0) outliers start: 85 outliers final: 47 residues processed: 272 average time/residue: 0.5096 time to fit residues: 166.9988 Evaluate side-chains 236 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 124 optimal weight: 5.9990 chunk 291 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 236 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 914 ASN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN B 913 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.079542 restraints weight = 41109.953| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.51 r_work: 0.2780 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28166 Z= 0.131 Angle : 0.605 19.765 38481 Z= 0.285 Chirality : 0.045 0.487 4533 Planarity : 0.003 0.044 4836 Dihedral : 7.754 113.753 5568 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 2.90 % Allowed : 22.89 % Favored : 74.20 % 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: -0.37 (0.14), residues: 3309 helix: 1.60 (0.20), residues: 732 sheet: 0.11 (0.19), residues: 720 loop : -1.19 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 847 TYR 0.017 0.001 TYR A1067 PHE 0.028 0.001 PHE C 823 TRP 0.009 0.001 TRP C 64 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00306 (28041) covalent geometry : angle 0.54899 (38166) SS BOND : bond 0.00310 ( 45) SS BOND : angle 1.24147 ( 90) hydrogen bonds : bond 0.03698 ( 1050) hydrogen bonds : angle 5.06758 ( 2982) Misc. bond : bond 0.00067 ( 5) link_BETA1-4 : bond 0.00391 ( 45) link_BETA1-4 : angle 2.02452 ( 135) link_NAG-ASN : bond 0.00824 ( 30) link_NAG-ASN : angle 4.58230 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 196 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8566 (mtp85) REVERT: A 1019 ARG cc_start: 0.8660 (tpt170) cc_final: 0.8452 (tpt170) REVERT: B 96 GLU cc_start: 0.7766 (pm20) cc_final: 0.7560 (pm20) REVERT: B 180 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: B 357 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8520 (ttt-90) REVERT: B 787 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7942 (mm-40) REVERT: C 24 LEU cc_start: 0.8942 (mt) cc_final: 0.8704 (tp) REVERT: C 78 ARG cc_start: 0.7423 (mmm-85) cc_final: 0.6942 (mmm160) REVERT: C 1050 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8692 (ptm) REVERT: C 1098 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8135 (p0) outliers start: 84 outliers final: 54 residues processed: 268 average time/residue: 0.4960 time to fit residues: 161.1078 Evaluate side-chains 244 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 272 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 259 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 241 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.078481 restraints weight = 41556.802| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.53 r_work: 0.2794 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28166 Z= 0.165 Angle : 0.620 19.695 38481 Z= 0.293 Chirality : 0.045 0.490 4533 Planarity : 0.003 0.045 4836 Dihedral : 7.493 112.978 5568 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 2.66 % Allowed : 23.27 % Favored : 74.07 % 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: -0.39 (0.14), residues: 3309 helix: 1.58 (0.20), residues: 732 sheet: 0.10 (0.19), residues: 720 loop : -1.20 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 847 TYR 0.027 0.001 TYR B1138 PHE 0.029 0.001 PHE C 823 TRP 0.009 0.001 TRP C 152 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00394 (28041) covalent geometry : angle 0.56397 (38166) SS BOND : bond 0.00338 ( 45) SS BOND : angle 1.36760 ( 90) hydrogen bonds : bond 0.03891 ( 1050) hydrogen bonds : angle 5.10221 ( 2982) Misc. bond : bond 0.00082 ( 5) link_BETA1-4 : bond 0.00377 ( 45) link_BETA1-4 : angle 2.04425 ( 135) link_NAG-ASN : bond 0.00816 ( 30) link_NAG-ASN : angle 4.60013 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 191 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8694 (mtt-85) cc_final: 0.8461 (mtt-85) REVERT: A 646 ARG cc_start: 0.8858 (ttp80) cc_final: 0.8572 (mtp85) REVERT: B 96 GLU cc_start: 0.7814 (pm20) cc_final: 0.7483 (pm20) REVERT: B 180 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: B 357 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8523 (ttt-90) REVERT: B 787 GLN cc_start: 0.8476 (mm-40) cc_final: 0.7847 (mm-40) REVERT: C 24 LEU cc_start: 0.8961 (mt) cc_final: 0.8725 (tp) REVERT: C 78 ARG cc_start: 0.7430 (mmm-85) cc_final: 0.6961 (mmm160) REVERT: C 755 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.6238 (mp10) REVERT: C 1050 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8699 (ptm) REVERT: C 1098 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8211 (p0) outliers start: 77 outliers final: 54 residues processed: 255 average time/residue: 0.5102 time to fit residues: 156.7232 Evaluate side-chains 245 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 186 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 324 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 75 optimal weight: 0.0010 chunk 5 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 304 optimal weight: 4.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.079642 restraints weight = 41390.745| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.51 r_work: 0.2815 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28166 Z= 0.132 Angle : 0.603 19.693 38481 Z= 0.285 Chirality : 0.045 0.476 4533 Planarity : 0.003 0.045 4836 Dihedral : 7.116 112.760 5568 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 2.32 % Allowed : 23.62 % Favored : 74.07 % 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: -0.30 (0.14), residues: 3309 helix: 1.63 (0.20), residues: 732 sheet: 0.22 (0.19), residues: 720 loop : -1.17 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 847 TYR 0.021 0.001 TYR A1067 PHE 0.029 0.001 PHE C 823 TRP 0.009 0.001 TRP C 152 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00309 (28041) covalent geometry : angle 0.54717 (38166) SS BOND : bond 0.00298 ( 45) SS BOND : angle 1.29111 ( 90) hydrogen bonds : bond 0.03689 ( 1050) hydrogen bonds : angle 5.04519 ( 2982) Misc. bond : bond 0.00069 ( 5) link_BETA1-4 : bond 0.00389 ( 45) link_BETA1-4 : angle 2.00467 ( 135) link_NAG-ASN : bond 0.00830 ( 30) link_NAG-ASN : angle 4.56132 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 192 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 190 ARG cc_start: 0.8658 (mtt-85) cc_final: 0.8402 (mtt-85) REVERT: A 646 ARG cc_start: 0.8840 (ttp80) cc_final: 0.8551 (mtp85) REVERT: B 51 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9045 (t) REVERT: B 96 GLU cc_start: 0.7822 (pm20) cc_final: 0.7416 (pm20) REVERT: B 180 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: B 357 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8554 (ttt-90) REVERT: B 787 GLN cc_start: 0.8469 (mm-40) cc_final: 0.7941 (mm-40) REVERT: B 847 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7315 (ptp-110) REVERT: C 24 LEU cc_start: 0.8950 (mt) cc_final: 0.8745 (tp) REVERT: C 78 ARG cc_start: 0.7402 (mmm-85) cc_final: 0.6941 (mmm160) REVERT: C 755 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6221 (mp10) REVERT: C 1050 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8686 (ptm) REVERT: C 1098 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8318 (p0) outliers start: 67 outliers final: 50 residues processed: 248 average time/residue: 0.5009 time to fit residues: 151.0453 Evaluate side-chains 240 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 282 optimal weight: 5.9990 chunk 256 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 206 optimal weight: 0.7980 chunk 312 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN C 23 GLN ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** C1135 ASN ** 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 = 0.3351 r_free = 0.3351 target = 0.108071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.079636 restraints weight = 41290.974| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.52 r_work: 0.2813 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 28166 Z= 0.145 Angle : 0.712 59.199 38481 Z= 0.373 Chirality : 0.045 0.476 4533 Planarity : 0.003 0.045 4836 Dihedral : 7.110 112.749 5568 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 2.07 % Allowed : 24.03 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3309 helix: 1.61 (0.20), residues: 732 sheet: 0.22 (0.19), residues: 720 loop : -1.17 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 847 TYR 0.021 0.001 TYR A1067 PHE 0.028 0.001 PHE C 823 TRP 0.008 0.001 TRP C 152 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00324 (28041) covalent geometry : angle 0.66532 (38166) SS BOND : bond 0.00313 ( 45) SS BOND : angle 1.36251 ( 90) hydrogen bonds : bond 0.03694 ( 1050) hydrogen bonds : angle 5.04873 ( 2982) Misc. bond : bond 0.00067 ( 5) link_BETA1-4 : bond 0.00436 ( 45) link_BETA1-4 : angle 2.02817 ( 135) link_NAG-ASN : bond 0.00828 ( 30) link_NAG-ASN : angle 4.56146 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 190 ARG cc_start: 0.8661 (mtt-85) cc_final: 0.8401 (mtt-85) REVERT: A 646 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8561 (mtp85) REVERT: B 51 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9047 (t) REVERT: B 96 GLU cc_start: 0.7822 (pm20) cc_final: 0.7502 (pm20) REVERT: B 180 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: B 357 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8557 (ttt-90) REVERT: B 787 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7936 (mm-40) REVERT: B 847 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7317 (ptp-110) REVERT: C 24 LEU cc_start: 0.8969 (mt) cc_final: 0.8734 (tp) REVERT: C 78 ARG cc_start: 0.7402 (mmm-85) cc_final: 0.6938 (mmm160) REVERT: C 755 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6221 (mp10) REVERT: C 1050 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8688 (ptm) REVERT: C 1098 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8320 (p0) outliers start: 60 outliers final: 51 residues processed: 235 average time/residue: 0.5189 time to fit residues: 147.6482 Evaluate side-chains 241 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 63 optimal weight: 0.9990 chunk 328 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 270 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN C 23 GLN ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** C1135 ASN ** 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 = 0.3351 r_free = 0.3351 target = 0.108070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.079689 restraints weight = 41185.739| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.51 r_work: 0.2827 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 28166 Z= 0.145 Angle : 0.712 59.199 38481 Z= 0.373 Chirality : 0.045 0.476 4533 Planarity : 0.003 0.045 4836 Dihedral : 7.110 112.749 5568 Min Nonbonded Distance : 1.575 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 1.97 % Allowed : 24.14 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3309 helix: 1.61 (0.20), residues: 732 sheet: 0.22 (0.19), residues: 720 loop : -1.17 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 847 TYR 0.021 0.001 TYR A1067 PHE 0.028 0.001 PHE C 823 TRP 0.008 0.001 TRP C 152 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00324 (28041) covalent geometry : angle 0.66532 (38166) SS BOND : bond 0.00313 ( 45) SS BOND : angle 1.36251 ( 90) hydrogen bonds : bond 0.03694 ( 1050) hydrogen bonds : angle 5.04873 ( 2982) Misc. bond : bond 0.00067 ( 5) link_BETA1-4 : bond 0.00436 ( 45) link_BETA1-4 : angle 2.02817 ( 135) link_NAG-ASN : bond 0.00828 ( 30) link_NAG-ASN : angle 4.56146 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7937.26 seconds wall clock time: 136 minutes 11.35 seconds (8171.35 seconds total)