Starting phenix.real_space_refine on Mon Sep 14 03:03:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jji_22352/09_2026/7jji_22352.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jji_22352/09_2026/7jji_22352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jji_22352/09_2026/7jji_22352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jji_22352/09_2026/7jji_22352.map" model { file = "/net/cci-nas-00/data/ceres_data/7jji_22352/09_2026/7jji_22352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jji_22352/09_2026/7jji_22352.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jji_22352/09_2026/7jji_22352.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jji_22352/09_2026/7jji_22352.cif" } resolution = 3.6 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= 0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17442 2.51 5 N 4437 2.21 5 O 5460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27459 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 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 chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'EIC': 1, 'NAG': 1, 'VCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'EIC': 1, 'NAG': 1, 'VCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'EIC': 1, 'NAG': 1, 'VCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.51, per 1000 atoms: 0.24 Number of scatterers: 27459 At special positions: 0 Unit cell: (156.4, 152.95, 177.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5460 8.00 N 4437 7.00 C 17442 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=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.07 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.07 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 B1502 " - " ASN B 331 " " NAG C1502 " - " ASN C 331 " " NAG D 1 " - " ASN A 61 " " NAG E 1 " - " ASN A 616 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 709 " " NAG H 1 " - " ASN A 717 " " 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 N 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 282 " " NAG P 1 " - " ASN A 165 " " NAG Q 1 " - " ASN A 17 " " NAG R 1 " - " ASN A 149 " " 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 a 1 " - " ASN B1134 " " NAG b 1 " - " ASN B 122 " " NAG c 1 " - " ASN B 234 " " NAG d 1 " - " ASN B 282 " " NAG e 1 " - " ASN B 165 " " NAG f 1 " - " ASN B 17 " " NAG g 1 " - " ASN B 149 " " NAG h 1 " - " ASN C 61 " " NAG i 1 " - " ASN C 616 " " NAG j 1 " - " ASN C 343 " " NAG k 1 " - " ASN C 709 " " NAG l 1 " - " ASN C 717 " " NAG m 1 " - " ASN C 801 " " NAG n 1 " - " ASN C1074 " " NAG o 1 " - " ASN C1098 " " NAG p 1 " - " ASN C1134 " " NAG q 1 " - " ASN C 122 " " NAG r 1 " - " ASN C 234 " " NAG s 1 " - " ASN C 282 " " NAG t 1 " - " ASN C 165 " " NAG u 1 " - " ASN C 17 " " NAG v 1 " - " ASN C 149 " Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 954.4 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: 78 helices and 51 sheets defined 25.5% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.847A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.599A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.616A 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 502 through 505 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 3.686A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 889 removed outlier: 3.571A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.014A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.847A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.599A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.616A 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 739 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.686A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (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 842 through 847 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 889 removed outlier: 3.572A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 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 1033 removed outlier: 4.015A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.847A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.599A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.616A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.686A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 842 through 847 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 889 removed outlier: 3.571A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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 1033 removed outlier: 4.015A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.711A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.348A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.101A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY A 142 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU A 154 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR A 144 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP A 152 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.197A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.922A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.936A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.873A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY A 142 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU A 154 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR A 144 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP A 152 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.587A 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 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.323A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.424A 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: 4.323A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.789A 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 660 removed outlier: 6.256A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.594A 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 711 through 728 removed outlier: 6.641A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.641A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.507A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.560A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.712A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 226 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.348A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.102A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR B 144 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP B 152 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.197A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.922A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.936A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.873A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR B 144 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP B 152 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.587A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.322A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.322A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.255A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.641A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.641A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.507A 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 1123 removed outlier: 3.560A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.711A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 226 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.348A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.101A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE C 140 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU C 156 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY C 142 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU C 154 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR C 144 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP C 152 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 removed outlier: 13.197A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.922A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.936A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.874A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE C 140 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU C 156 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY C 142 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU C 154 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR C 144 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP C 152 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.587A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.322A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.424A 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: 4.322A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.789A 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 660 removed outlier: 6.256A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.597A 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 728 removed outlier: 6.641A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.641A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.508A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.560A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1156 hydrogen bonds defined for protein. 3072 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.36 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5449 1.32 - 1.46: 10163 1.46 - 1.61: 12291 1.61 - 1.75: 30 1.75 - 1.90: 129 Bond restraints: 28062 Sorted by residual: bond pdb=" C27 VCG A1302 " pdb=" C28 VCG A1302 " ideal model delta sigma weight residual 1.527 1.291 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C27 VCG C1503 " pdb=" C28 VCG C1503 " ideal model delta sigma weight residual 1.527 1.291 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C27 VCG B1503 " pdb=" C28 VCG B1503 " ideal model delta sigma weight residual 1.527 1.291 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C29 VCG A1302 " pdb=" O30 VCG A1302 " ideal model delta sigma weight residual 1.397 1.529 -0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" C29 VCG B1503 " pdb=" O30 VCG B1503 " ideal model delta sigma weight residual 1.397 1.529 -0.132 2.00e-02 2.50e+03 4.33e+01 ... (remaining 28057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.96: 38004 6.96 - 13.92: 135 13.92 - 20.88: 0 20.88 - 27.84: 0 27.84 - 34.80: 3 Bond angle restraints: 38142 Sorted by residual: angle pdb=" C2 NAG A1301 " pdb=" N2 NAG A1301 " pdb=" C7 NAG A1301 " ideal model delta sigma weight residual 124.56 159.36 -34.80 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C2 NAG C1502 " pdb=" N2 NAG C1502 " pdb=" C7 NAG C1502 " ideal model delta sigma weight residual 124.56 159.34 -34.78 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C2 NAG B1502 " pdb=" N2 NAG B1502 " pdb=" C7 NAG B1502 " ideal model delta sigma weight residual 124.56 159.28 -34.72 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C PRO B 862 " pdb=" N PRO B 863 " pdb=" CA PRO B 863 " ideal model delta sigma weight residual 120.03 127.98 -7.95 9.90e-01 1.02e+00 6.44e+01 angle pdb=" C PRO C 862 " pdb=" N PRO C 863 " pdb=" CA PRO C 863 " ideal model delta sigma weight residual 120.03 127.97 -7.94 9.90e-01 1.02e+00 6.43e+01 ... (remaining 38137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 15345 17.54 - 35.07: 492 35.07 - 52.61: 135 52.61 - 70.14: 51 70.14 - 87.68: 18 Dihedral angle restraints: 16041 sinusoidal: 6366 harmonic: 9675 Sorted by residual: dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual 93.00 150.80 -57.80 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 150.80 -57.80 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual 93.00 150.80 -57.80 1 1.00e+01 1.00e-02 4.48e+01 ... (remaining 16038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3111 0.106 - 0.212: 970 0.212 - 0.319: 299 0.319 - 0.425: 127 0.425 - 0.531: 56 Chirality restraints: 4563 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.55e+02 chirality pdb=" C1 NAG k 2 " pdb=" O4 NAG k 1 " pdb=" C2 NAG k 2 " pdb=" O5 NAG k 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.51e+02 ... (remaining 4560 not shown) Planarity restraints: 4863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " -0.056 2.00e-02 2.50e+03 6.07e-02 4.60e+01 pdb=" CG ASN A 122 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " 0.097 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 122 " -0.056 2.00e-02 2.50e+03 6.05e-02 4.58e+01 pdb=" CG ASN C 122 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 122 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 122 " 0.097 2.00e-02 2.50e+03 pdb=" C1 NAG q 1 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " 0.056 2.00e-02 2.50e+03 6.05e-02 4.57e+01 pdb=" CG ASN B 122 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " -0.097 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.073 2.00e-02 2.50e+03 ... (remaining 4860 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 11173 2.90 - 3.40: 24895 3.40 - 3.90: 45726 3.90 - 4.40: 53481 4.40 - 4.90: 85321 Nonbonded interactions: 220596 Sorted by model distance: nonbonded pdb=" OE2 GLU C 725 " pdb=" NZ LYS C1028 " model vdw 2.399 3.120 nonbonded pdb=" OE2 GLU A 725 " pdb=" NZ LYS A1028 " model vdw 2.399 3.120 nonbonded pdb=" OE2 GLU B 725 " pdb=" NZ LYS B1028 " model vdw 2.399 3.120 nonbonded pdb=" N PRO A 600 " pdb=" O PRO A 600 " model vdw 2.438 2.496 nonbonded pdb=" N PRO C 600 " pdb=" O PRO C 600 " model vdw 2.438 2.496 ... (remaining 220591 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1146) selection = (chain 'B' and resid 14 through 1146) selection = (chain 'C' and resid 14 through 1146) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.510 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 : 0.021 0.236 28200 Z= 1.130 Angle : 1.814 34.799 38511 Z= 1.168 Chirality : 0.134 0.531 4563 Planarity : 0.008 0.058 4815 Dihedral : 10.582 87.675 9696 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.21 % Allowed : 0.41 % Favored : 99.38 % 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 (0.13), residues: 3309 helix: 0.11 (0.17), residues: 702 sheet: 1.16 (0.19), residues: 684 loop : 0.24 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.073 0.008 TYR A 707 PHE 0.031 0.006 PHE A 888 TRP 0.030 0.008 TRP A 353 HIS 0.006 0.002 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.02105 / 1.11 (28062) covalent geometry : angle 1.78428 / 1.17 (38142) SS BOND : bond 0.01270 / 0.87 ( 45) SS BOND : angle 2.91107 / 2.04 ( 90) hydrogen bonds : bond 0.17190 / 11.56 ( 1078) hydrogen bonds : angle 8.17195 / 5.68 ( 3072) link_BETA1-4 : bond 0.07494 / 4.85 ( 45) link_BETA1-4 : angle 5.25520 / 3.52 ( 135) link_NAG-ASN : bond 0.07726 / 5.06 ( 48) link_NAG-ASN : angle 2.39478 / 1.67 ( 144) *********************** 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 546 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 540 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8444 (p) cc_final: 0.7909 (t) REVERT: A 216 LEU cc_start: 0.8299 (mt) cc_final: 0.7652 (tp) REVERT: A 312 ILE cc_start: 0.8858 (mm) cc_final: 0.8346 (tt) REVERT: A 523 THR cc_start: 0.8226 (p) cc_final: 0.7860 (t) REVERT: A 695 TYR cc_start: 0.8897 (p90) cc_final: 0.8660 (p90) REVERT: A 1037 SER cc_start: 0.8749 (t) cc_final: 0.8294 (m) REVERT: B 19 THR cc_start: 0.8305 (p) cc_final: 0.7841 (t) REVERT: B 46 SER cc_start: 0.9148 (m) cc_final: 0.8908 (t) REVERT: B 110 LEU cc_start: 0.8464 (mt) cc_final: 0.8234 (mp) REVERT: B 290 ASP cc_start: 0.7935 (t0) cc_final: 0.7631 (t0) REVERT: B 312 ILE cc_start: 0.8884 (mm) cc_final: 0.8487 (tt) REVERT: B 523 THR cc_start: 0.8228 (p) cc_final: 0.7880 (t) REVERT: B 707 TYR cc_start: 0.8307 (t80) cc_final: 0.7985 (t80) REVERT: B 900 MET cc_start: 0.8700 (mtt) cc_final: 0.8399 (mtp) REVERT: B 1037 SER cc_start: 0.8750 (t) cc_final: 0.8313 (m) REVERT: C 19 THR cc_start: 0.8339 (p) cc_final: 0.7835 (t) REVERT: C 46 SER cc_start: 0.9118 (m) cc_final: 0.8657 (t) REVERT: C 197 ILE cc_start: 0.8661 (mt) cc_final: 0.8390 (mm) REVERT: C 312 ILE cc_start: 0.8912 (mm) cc_final: 0.8509 (tt) REVERT: C 360 ASN cc_start: 0.8602 (m-40) cc_final: 0.8384 (m-40) REVERT: C 523 THR cc_start: 0.8253 (p) cc_final: 0.8049 (t) REVERT: C 737 ASP cc_start: 0.7898 (t0) cc_final: 0.7643 (t0) REVERT: C 740 MET cc_start: 0.8605 (mmm) cc_final: 0.7820 (tpp) REVERT: C 900 MET cc_start: 0.8944 (mtt) cc_final: 0.8710 (mtp) outliers start: 6 outliers final: 0 residues processed: 546 average time/residue: 0.1955 time to fit residues: 167.0551 Evaluate side-chains 195 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 GLN A 519 HIS A 544 ASN A 690 GLN A 755 GLN A 913 GLN B 493 GLN B 519 HIS B 544 ASN B 606 ASN B 913 GLN B 957 GLN C 519 HIS C 544 ASN C 606 ASN C 690 GLN C 955 ASN C 957 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.126394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106601 restraints weight = 45445.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.110337 restraints weight = 22755.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.112784 restraints weight = 14477.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114394 restraints weight = 10640.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115469 restraints weight = 8574.988| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28200 Z= 0.182 Angle : 0.765 12.962 38511 Z= 0.393 Chirality : 0.050 0.449 4563 Planarity : 0.004 0.035 4815 Dihedral : 7.957 58.603 3777 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.83 % Allowed : 5.12 % Favored : 93.05 % 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: 0.87 (0.14), residues: 3309 helix: 1.88 (0.20), residues: 681 sheet: 0.81 (0.20), residues: 681 loop : 0.08 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1014 TYR 0.042 0.002 TYR C 707 PHE 0.023 0.002 PHE B1095 TRP 0.017 0.002 TRP A 152 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (28062) covalent geometry : angle 0.71145 / 0.38 (38142) SS BOND : bond 0.00322 / 0.19 ( 45) SS BOND : angle 1.78561 / 1.29 ( 90) hydrogen bonds : bond 0.06526 / 4.35 ( 1078) hydrogen bonds : angle 6.39546 / 4.47 ( 3072) link_BETA1-4 : bond 0.00719 / 0.48 ( 45) link_BETA1-4 : angle 3.20699 / 2.18 ( 135) link_NAG-ASN : bond 0.00682 / 0.46 ( 48) link_NAG-ASN : angle 3.28235 / 2.29 ( 144) *********************** 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 270 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8681 (p) cc_final: 0.8309 (t) REVERT: A 332 ILE cc_start: 0.9212 (mm) cc_final: 0.8943 (mp) REVERT: A 523 THR cc_start: 0.8274 (p) cc_final: 0.7755 (t) REVERT: A 737 ASP cc_start: 0.8348 (t0) cc_final: 0.8133 (t0) REVERT: A 1031 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: A 1037 SER cc_start: 0.8961 (t) cc_final: 0.8516 (m) REVERT: B 19 THR cc_start: 0.8580 (p) cc_final: 0.8278 (t) REVERT: B 290 ASP cc_start: 0.8201 (t0) cc_final: 0.7739 (t0) REVERT: B 523 THR cc_start: 0.8218 (p) cc_final: 0.7709 (t) REVERT: B 614 ASP cc_start: 0.7731 (p0) cc_final: 0.7493 (p0) REVERT: B 646 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7224 (ttp80) REVERT: B 707 TYR cc_start: 0.8388 (t80) cc_final: 0.7669 (t80) REVERT: B 760 CYS cc_start: 0.6259 (OUTLIER) cc_final: 0.6013 (t) REVERT: B 1037 SER cc_start: 0.9118 (t) cc_final: 0.8547 (m) REVERT: B 1135 ASN cc_start: 0.8471 (t0) cc_final: 0.8160 (t0) REVERT: C 19 THR cc_start: 0.8686 (p) cc_final: 0.8376 (t) REVERT: C 737 ASP cc_start: 0.8309 (t0) cc_final: 0.7873 (t0) REVERT: C 740 MET cc_start: 0.8746 (mmm) cc_final: 0.8515 (mmm) REVERT: C 760 CYS cc_start: 0.6493 (OUTLIER) cc_final: 0.6198 (t) REVERT: C 823 PHE cc_start: 0.8053 (t80) cc_final: 0.7785 (t80) REVERT: C 1037 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8627 (m) outliers start: 53 outliers final: 34 residues processed: 264 average time/residue: 0.1710 time to fit residues: 74.2773 Evaluate side-chains 205 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 182 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 232 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 207 HIS A 519 HIS A 655 HIS A 913 GLN B 115 GLN B 498 GLN B 519 HIS B 606 ASN B 655 HIS B 913 GLN B 926 GLN B 955 ASN B1048 HIS C 115 GLN C 207 HIS C 519 HIS C 606 ASN C 655 HIS C 913 GLN C 926 GLN C 955 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.120925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.101288 restraints weight = 46324.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104823 restraints weight = 23493.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107120 restraints weight = 15132.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108678 restraints weight = 11283.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109702 restraints weight = 9159.501| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28200 Z= 0.221 Angle : 0.690 11.843 38511 Z= 0.352 Chirality : 0.048 0.398 4563 Planarity : 0.004 0.035 4815 Dihedral : 7.740 60.768 3777 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.66 % Allowed : 5.98 % Favored : 91.36 % 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: 0.50 (0.14), residues: 3309 helix: 1.72 (0.19), residues: 702 sheet: 0.63 (0.18), residues: 732 loop : -0.29 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1039 TYR 0.024 0.002 TYR C 707 PHE 0.024 0.002 PHE B 329 TRP 0.015 0.002 TRP A 436 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (28062) covalent geometry : angle 0.64904 / 0.34 (38142) SS BOND : bond 0.00398 / 0.25 ( 45) SS BOND : angle 1.47913 / 1.06 ( 90) hydrogen bonds : bond 0.05419 / 3.65 ( 1078) hydrogen bonds : angle 5.82987 / 4.09 ( 3072) link_BETA1-4 : bond 0.00453 / 0.29 ( 45) link_BETA1-4 : angle 2.53597 / 1.70 ( 135) link_NAG-ASN : bond 0.00435 / 0.29 ( 48) link_NAG-ASN : angle 2.86795 / 2.02 ( 144) *********************** 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 259 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 182 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8583 (p) cc_final: 0.8216 (t) REVERT: A 332 ILE cc_start: 0.9183 (mm) cc_final: 0.8916 (mp) REVERT: A 737 ASP cc_start: 0.8302 (t0) cc_final: 0.8043 (t0) REVERT: A 1037 SER cc_start: 0.9189 (t) cc_final: 0.8793 (m) REVERT: A 1043 CYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7508 (m) REVERT: B 19 THR cc_start: 0.8499 (p) cc_final: 0.8198 (t) REVERT: B 290 ASP cc_start: 0.8504 (t0) cc_final: 0.8244 (t70) REVERT: B 458 LYS cc_start: 0.9155 (mttt) cc_final: 0.8923 (mtpp) REVERT: B 614 ASP cc_start: 0.7879 (p0) cc_final: 0.7670 (p0) REVERT: B 646 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7714 (ttp80) REVERT: B 760 CYS cc_start: 0.6092 (OUTLIER) cc_final: 0.5836 (t) REVERT: B 900 MET cc_start: 0.8622 (mtp) cc_final: 0.8324 (mtp) REVERT: B 1037 SER cc_start: 0.9076 (t) cc_final: 0.8536 (m) REVERT: C 19 THR cc_start: 0.8607 (p) cc_final: 0.8319 (t) REVERT: C 332 ILE cc_start: 0.9248 (mm) cc_final: 0.9009 (mp) REVERT: C 760 CYS cc_start: 0.6516 (OUTLIER) cc_final: 0.6249 (t) REVERT: C 823 PHE cc_start: 0.8031 (t80) cc_final: 0.7776 (t80) REVERT: C 900 MET cc_start: 0.8729 (mtp) cc_final: 0.8413 (mtp) REVERT: C 1037 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8770 (m) REVERT: C 1043 CYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7859 (m) REVERT: C 1050 MET cc_start: 0.6988 (ptm) cc_final: 0.6718 (ptm) outliers start: 77 outliers final: 50 residues processed: 254 average time/residue: 0.1800 time to fit residues: 74.8168 Evaluate side-chains 196 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 140 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1136 THR 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 216 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 297 optimal weight: 6.9990 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 519 HIS B 926 GLN C 519 HIS C 606 ASN C 913 GLN C 926 GLN C 955 ASN C1048 HIS C1142 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093915 restraints weight = 45063.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097671 restraints weight = 23135.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.100099 restraints weight = 15111.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.101700 restraints weight = 11365.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102777 restraints weight = 9320.193| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28200 Z= 0.213 Angle : 0.658 11.131 38511 Z= 0.334 Chirality : 0.047 0.389 4563 Planarity : 0.004 0.045 4815 Dihedral : 7.669 60.810 3777 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.84 % Allowed : 6.81 % Favored : 90.35 % 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: 0.24 (0.14), residues: 3309 helix: 1.56 (0.19), residues: 723 sheet: 0.39 (0.18), residues: 744 loop : -0.48 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.026 0.002 TYR C 248 PHE 0.020 0.002 PHE B 329 TRP 0.014 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (28062) covalent geometry : angle 0.62118 / 0.33 (38142) SS BOND : bond 0.00333 / 0.22 ( 45) SS BOND : angle 1.22415 / 0.89 ( 90) hydrogen bonds : bond 0.05114 / 3.43 ( 1078) hydrogen bonds : angle 5.64457 / 3.96 ( 3072) link_BETA1-4 : bond 0.00391 / 0.25 ( 45) link_BETA1-4 : angle 2.39381 / 1.61 ( 135) link_NAG-ASN : bond 0.00363 / 0.24 ( 48) link_NAG-ASN : angle 2.71439 / 1.90 ( 144) *********************** 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 253 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 171 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8571 (p) cc_final: 0.8214 (t) REVERT: A 332 ILE cc_start: 0.9146 (mm) cc_final: 0.8911 (mp) REVERT: A 737 ASP cc_start: 0.8271 (t0) cc_final: 0.8024 (t0) REVERT: A 1037 SER cc_start: 0.9266 (t) cc_final: 0.8875 (m) REVERT: A 1043 CYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7598 (m) REVERT: B 19 THR cc_start: 0.8449 (p) cc_final: 0.8153 (t) REVERT: B 458 LYS cc_start: 0.9142 (mttt) cc_final: 0.8935 (mtpp) REVERT: B 646 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7771 (ttp80) REVERT: B 760 CYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5954 (t) REVERT: B 1037 SER cc_start: 0.9196 (t) cc_final: 0.8833 (m) REVERT: B 1042 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.7963 (t80) REVERT: C 19 THR cc_start: 0.8575 (p) cc_final: 0.8283 (t) REVERT: C 249 LEU cc_start: 0.9006 (mt) cc_final: 0.8735 (tt) REVERT: C 332 ILE cc_start: 0.9240 (mm) cc_final: 0.9017 (mp) REVERT: C 458 LYS cc_start: 0.9118 (mttt) cc_final: 0.8911 (mtmm) REVERT: C 483 VAL cc_start: 0.8596 (t) cc_final: 0.8352 (p) REVERT: C 740 MET cc_start: 0.9088 (mmm) cc_final: 0.8392 (mtp) REVERT: C 760 CYS cc_start: 0.6406 (OUTLIER) cc_final: 0.6165 (t) REVERT: C 823 PHE cc_start: 0.8072 (t80) cc_final: 0.7776 (t80) REVERT: C 900 MET cc_start: 0.8707 (mtp) cc_final: 0.8341 (mtp) REVERT: C 1037 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.8823 (m) REVERT: C 1043 CYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7870 (m) outliers start: 82 outliers final: 54 residues processed: 241 average time/residue: 0.1780 time to fit residues: 71.2077 Evaluate side-chains 208 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 147 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR 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 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 236 optimal weight: 0.0770 chunk 225 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS A 913 GLN A 955 ASN B 501 ASN B 519 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 519 HIS C 606 ASN C 913 GLN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.116531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096222 restraints weight = 44182.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099938 restraints weight = 22414.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.102352 restraints weight = 14466.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.103912 restraints weight = 10780.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.104997 restraints weight = 8807.652| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28200 Z= 0.124 Angle : 0.589 10.077 38511 Z= 0.297 Chirality : 0.045 0.360 4563 Planarity : 0.003 0.051 4815 Dihedral : 7.351 61.168 3777 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.32 % Allowed : 8.02 % Favored : 89.66 % 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: 0.36 (0.14), residues: 3309 helix: 1.88 (0.20), residues: 705 sheet: 0.42 (0.19), residues: 711 loop : -0.44 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1107 TYR 0.025 0.001 TYR B 248 PHE 0.019 0.001 PHE A 823 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (28062) covalent geometry : angle 0.55385 / 0.29 (38142) SS BOND : bond 0.00230 / 0.15 ( 45) SS BOND : angle 1.07301 / 0.78 ( 90) hydrogen bonds : bond 0.04510 / 3.04 ( 1078) hydrogen bonds : angle 5.38545 / 3.79 ( 3072) link_BETA1-4 : bond 0.00460 / 0.30 ( 45) link_BETA1-4 : angle 2.28675 / 1.52 ( 135) link_NAG-ASN : bond 0.00331 / 0.23 ( 48) link_NAG-ASN : angle 2.44627 / 1.73 ( 144) *********************** 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 241 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8505 (p) cc_final: 0.8164 (t) REVERT: A 332 ILE cc_start: 0.9120 (mm) cc_final: 0.8915 (mp) REVERT: A 737 ASP cc_start: 0.8228 (t0) cc_final: 0.7955 (t0) REVERT: A 1037 SER cc_start: 0.9267 (t) cc_final: 0.8921 (m) REVERT: B 19 THR cc_start: 0.8430 (p) cc_final: 0.8102 (t) REVERT: B 458 LYS cc_start: 0.9151 (mttt) cc_final: 0.8937 (mtpp) REVERT: B 646 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7796 (ttp80) REVERT: B 760 CYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5838 (t) REVERT: B 1037 SER cc_start: 0.9148 (t) cc_final: 0.8631 (m) REVERT: B 1042 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8094 (t80) REVERT: C 19 THR cc_start: 0.8453 (p) cc_final: 0.8161 (t) REVERT: C 111 ASP cc_start: 0.8154 (t0) cc_final: 0.7783 (t0) REVERT: C 332 ILE cc_start: 0.9213 (mm) cc_final: 0.8999 (mp) REVERT: C 458 LYS cc_start: 0.9120 (mttt) cc_final: 0.8919 (mtmm) REVERT: C 740 MET cc_start: 0.9035 (mmm) cc_final: 0.8428 (mtp) REVERT: C 760 CYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5784 (t) REVERT: C 823 PHE cc_start: 0.8057 (t80) cc_final: 0.7760 (t80) REVERT: C 1037 SER cc_start: 0.9263 (OUTLIER) cc_final: 0.8825 (m) REVERT: C 1043 CYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7756 (m) REVERT: C 1135 ASN cc_start: 0.8555 (t0) cc_final: 0.8331 (t0) outliers start: 67 outliers final: 50 residues processed: 233 average time/residue: 0.1693 time to fit residues: 66.3263 Evaluate side-chains 205 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 149 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL 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 136 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 256 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 281 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS A 777 ASN B 519 HIS B 955 ASN C 519 HIS C 606 ASN C 913 GLN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.090704 restraints weight = 45601.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094297 restraints weight = 23474.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.096682 restraints weight = 15342.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.098223 restraints weight = 11500.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.099247 restraints weight = 9446.260| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28200 Z= 0.143 Angle : 0.585 10.444 38511 Z= 0.295 Chirality : 0.045 0.355 4563 Planarity : 0.003 0.053 4815 Dihedral : 7.195 61.416 3777 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.32 % Allowed : 8.82 % Favored : 88.87 % 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: 0.33 (0.14), residues: 3309 helix: 1.92 (0.20), residues: 705 sheet: 0.39 (0.19), residues: 726 loop : -0.50 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1107 TYR 0.021 0.001 TYR B 707 PHE 0.016 0.001 PHE A 823 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (28062) covalent geometry : angle 0.55109 / 0.29 (38142) SS BOND : bond 0.00247 / 0.17 ( 45) SS BOND : angle 1.05722 / 0.78 ( 90) hydrogen bonds : bond 0.04443 / 3.00 ( 1078) hydrogen bonds : angle 5.30497 / 3.73 ( 3072) link_BETA1-4 : bond 0.00413 / 0.27 ( 45) link_BETA1-4 : angle 2.21493 / 1.48 ( 135) link_NAG-ASN : bond 0.00308 / 0.21 ( 48) link_NAG-ASN : angle 2.39531 / 1.69 ( 144) *********************** 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 229 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 162 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8476 (p) cc_final: 0.8184 (t) REVERT: A 737 ASP cc_start: 0.8245 (t0) cc_final: 0.7911 (t0) REVERT: A 790 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8248 (mmtm) REVERT: A 1037 SER cc_start: 0.9293 (t) cc_final: 0.8948 (m) REVERT: B 19 THR cc_start: 0.8477 (p) cc_final: 0.8175 (t) REVERT: B 111 ASP cc_start: 0.8266 (t0) cc_final: 0.8010 (t0) REVERT: B 458 LYS cc_start: 0.9227 (mttt) cc_final: 0.8979 (mtpp) REVERT: B 646 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7868 (ttp80) REVERT: B 760 CYS cc_start: 0.6128 (OUTLIER) cc_final: 0.5835 (t) REVERT: B 900 MET cc_start: 0.8407 (mtp) cc_final: 0.8143 (mtp) REVERT: B 1037 SER cc_start: 0.9159 (t) cc_final: 0.8804 (m) REVERT: B 1042 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.7992 (t80) REVERT: B 1142 GLN cc_start: 0.8100 (tp40) cc_final: 0.7876 (tp40) REVERT: C 19 THR cc_start: 0.8466 (p) cc_final: 0.8199 (t) REVERT: C 111 ASP cc_start: 0.8215 (t0) cc_final: 0.7790 (t0) REVERT: C 332 ILE cc_start: 0.9217 (mm) cc_final: 0.8991 (mp) REVERT: C 458 LYS cc_start: 0.9200 (mttt) cc_final: 0.8886 (mtpp) REVERT: C 483 VAL cc_start: 0.8561 (t) cc_final: 0.8311 (p) REVERT: C 740 MET cc_start: 0.9028 (mmm) cc_final: 0.8477 (mtp) REVERT: C 760 CYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5833 (t) REVERT: C 823 PHE cc_start: 0.8089 (t80) cc_final: 0.7753 (t80) REVERT: C 1037 SER cc_start: 0.9314 (OUTLIER) cc_final: 0.8881 (m) REVERT: C 1043 CYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7934 (m) outliers start: 67 outliers final: 49 residues processed: 221 average time/residue: 0.1685 time to fit residues: 61.6710 Evaluate side-chains 197 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL 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 228 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 256 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 chunk 20 optimal weight: 0.0470 chunk 323 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS A 913 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 777 ASN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.110235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.089837 restraints weight = 45137.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.093460 restraints weight = 22500.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095853 restraints weight = 14410.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097401 restraints weight = 10656.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098439 restraints weight = 8692.792| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28200 Z= 0.139 Angle : 0.575 9.557 38511 Z= 0.290 Chirality : 0.045 0.347 4563 Planarity : 0.003 0.053 4815 Dihedral : 7.045 61.379 3777 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.28 % Allowed : 9.02 % Favored : 88.69 % 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: 1.96 (0.20), residues: 705 sheet: 0.27 (0.19), residues: 744 loop : -0.51 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 847 TYR 0.024 0.001 TYR C 248 PHE 0.016 0.001 PHE A 329 TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (28062) covalent geometry : angle 0.54346 / 0.28 (38142) SS BOND : bond 0.00245 / 0.17 ( 45) SS BOND : angle 0.99451 / 0.72 ( 90) hydrogen bonds : bond 0.04331 / 2.93 ( 1078) hydrogen bonds : angle 5.23978 / 3.68 ( 3072) link_BETA1-4 : bond 0.00413 / 0.27 ( 45) link_BETA1-4 : angle 2.16339 / 1.44 ( 135) link_NAG-ASN : bond 0.00315 / 0.21 ( 48) link_NAG-ASN : angle 2.30835 / 1.64 ( 144) *********************** 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 225 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 159 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8410 (p) cc_final: 0.8127 (t) REVERT: A 737 ASP cc_start: 0.8246 (t0) cc_final: 0.7908 (t0) REVERT: A 1037 SER cc_start: 0.9325 (t) cc_final: 0.8980 (m) REVERT: B 19 THR cc_start: 0.8432 (p) cc_final: 0.8130 (t) REVERT: B 111 ASP cc_start: 0.8265 (t0) cc_final: 0.7992 (t0) REVERT: B 458 LYS cc_start: 0.9224 (mttt) cc_final: 0.8923 (mtpp) REVERT: B 646 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7885 (ttp80) REVERT: B 760 CYS cc_start: 0.5965 (OUTLIER) cc_final: 0.5698 (t) REVERT: B 900 MET cc_start: 0.8377 (mtp) cc_final: 0.8068 (mtp) REVERT: B 1037 SER cc_start: 0.9162 (t) cc_final: 0.8806 (m) REVERT: B 1043 CYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7834 (m) REVERT: B 1142 GLN cc_start: 0.8140 (tp40) cc_final: 0.7907 (tp40) REVERT: C 19 THR cc_start: 0.8410 (p) cc_final: 0.8178 (t) REVERT: C 111 ASP cc_start: 0.8175 (t0) cc_final: 0.7610 (t0) REVERT: C 332 ILE cc_start: 0.9211 (mm) cc_final: 0.8999 (mp) REVERT: C 458 LYS cc_start: 0.9197 (mttt) cc_final: 0.8882 (mtpp) REVERT: C 483 VAL cc_start: 0.8560 (t) cc_final: 0.8314 (p) REVERT: C 740 MET cc_start: 0.8993 (mmm) cc_final: 0.8511 (mtp) REVERT: C 760 CYS cc_start: 0.6116 (OUTLIER) cc_final: 0.5887 (t) REVERT: C 779 GLN cc_start: 0.8223 (tt0) cc_final: 0.7983 (tt0) REVERT: C 823 PHE cc_start: 0.8070 (t80) cc_final: 0.7714 (t80) REVERT: C 1037 SER cc_start: 0.9317 (OUTLIER) cc_final: 0.8898 (m) outliers start: 66 outliers final: 53 residues processed: 216 average time/residue: 0.1663 time to fit residues: 60.1036 Evaluate side-chains 204 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 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 41 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 313 optimal weight: 1.9990 chunk 307 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 123 optimal weight: 0.0170 chunk 159 optimal weight: 0.6980 chunk 327 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 955 ASN C 606 ASN C 777 ASN C 913 GLN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.111108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.090654 restraints weight = 45422.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094299 restraints weight = 22497.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.096695 restraints weight = 14375.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.098258 restraints weight = 10651.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.099255 restraints weight = 8657.701| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28200 Z= 0.117 Angle : 0.558 9.183 38511 Z= 0.281 Chirality : 0.044 0.339 4563 Planarity : 0.003 0.054 4815 Dihedral : 6.900 61.661 3777 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.21 % Allowed : 9.54 % Favored : 88.24 % 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: 0.33 (0.14), residues: 3309 helix: 2.03 (0.20), residues: 705 sheet: 0.26 (0.19), residues: 723 loop : -0.49 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 847 TYR 0.024 0.001 TYR C 248 PHE 0.016 0.001 PHE A 823 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (28062) covalent geometry : angle 0.52645 / 0.27 (38142) SS BOND : bond 0.00211 / 0.14 ( 45) SS BOND : angle 0.94102 / 0.68 ( 90) hydrogen bonds : bond 0.04178 / 2.83 ( 1078) hydrogen bonds : angle 5.15611 / 3.62 ( 3072) link_BETA1-4 : bond 0.00432 / 0.28 ( 45) link_BETA1-4 : angle 2.12848 / 1.41 ( 135) link_NAG-ASN : bond 0.00292 / 0.20 ( 48) link_NAG-ASN : angle 2.22085 / 1.57 ( 144) *********************** 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 218 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 154 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8421 (p) cc_final: 0.8162 (t) REVERT: A 572 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8558 (p) REVERT: A 737 ASP cc_start: 0.8259 (t0) cc_final: 0.7922 (t0) REVERT: A 1037 SER cc_start: 0.9326 (t) cc_final: 0.8981 (m) REVERT: B 19 THR cc_start: 0.8420 (p) cc_final: 0.8125 (t) REVERT: B 111 ASP cc_start: 0.8178 (t0) cc_final: 0.7892 (t0) REVERT: B 458 LYS cc_start: 0.9223 (mttt) cc_final: 0.8935 (mtpp) REVERT: B 646 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7934 (ttp80) REVERT: B 760 CYS cc_start: 0.5891 (OUTLIER) cc_final: 0.5603 (t) REVERT: B 900 MET cc_start: 0.8362 (mtp) cc_final: 0.8074 (mtp) REVERT: B 1037 SER cc_start: 0.9160 (t) cc_final: 0.8791 (m) REVERT: B 1042 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8068 (t80) REVERT: B 1043 CYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8034 (m) REVERT: B 1142 GLN cc_start: 0.8162 (tp40) cc_final: 0.7949 (tp40) REVERT: C 19 THR cc_start: 0.8385 (p) cc_final: 0.8143 (t) REVERT: C 111 ASP cc_start: 0.8168 (t0) cc_final: 0.7611 (t0) REVERT: C 332 ILE cc_start: 0.9176 (mm) cc_final: 0.8948 (mp) REVERT: C 458 LYS cc_start: 0.9192 (mttt) cc_final: 0.8870 (mtpp) REVERT: C 483 VAL cc_start: 0.8546 (t) cc_final: 0.8300 (p) REVERT: C 740 MET cc_start: 0.8966 (mmm) cc_final: 0.8503 (mtp) REVERT: C 760 CYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5818 (t) REVERT: C 823 PHE cc_start: 0.8049 (t80) cc_final: 0.7693 (t80) REVERT: C 1037 SER cc_start: 0.9327 (OUTLIER) cc_final: 0.8891 (m) outliers start: 64 outliers final: 49 residues processed: 211 average time/residue: 0.1709 time to fit residues: 60.5583 Evaluate side-chains 202 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 146 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 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 307 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 322 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 137 optimal weight: 0.1980 chunk 112 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 913 GLN B 955 ASN C 606 ASN C 913 GLN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091158 restraints weight = 45496.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094785 restraints weight = 22526.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097199 restraints weight = 14412.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098741 restraints weight = 10642.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.099790 restraints weight = 8660.493| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28200 Z= 0.115 Angle : 0.548 9.002 38511 Z= 0.276 Chirality : 0.044 0.332 4563 Planarity : 0.003 0.054 4815 Dihedral : 6.735 61.651 3777 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.21 % Allowed : 9.54 % Favored : 88.24 % 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: 0.38 (0.14), residues: 3309 helix: 2.06 (0.20), residues: 720 sheet: 0.29 (0.19), residues: 723 loop : -0.47 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 847 TYR 0.026 0.001 TYR B 707 PHE 0.022 0.001 PHE B 823 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (28062) covalent geometry : angle 0.51779 / 0.27 (38142) SS BOND : bond 0.00206 / 0.14 ( 45) SS BOND : angle 0.92108 / 0.67 ( 90) hydrogen bonds : bond 0.04058 / 2.75 ( 1078) hydrogen bonds : angle 5.10067 / 3.59 ( 3072) link_BETA1-4 : bond 0.00431 / 0.28 ( 45) link_BETA1-4 : angle 2.08912 / 1.38 ( 135) link_NAG-ASN : bond 0.00282 / 0.19 ( 48) link_NAG-ASN : angle 2.14942 / 1.52 ( 144) *********************** 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 218 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 154 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8365 (p) cc_final: 0.8095 (t) REVERT: A 572 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8578 (p) REVERT: A 737 ASP cc_start: 0.8223 (t0) cc_final: 0.7888 (t0) REVERT: A 1037 SER cc_start: 0.9312 (t) cc_final: 0.8970 (m) REVERT: B 19 THR cc_start: 0.8367 (p) cc_final: 0.8080 (t) REVERT: B 111 ASP cc_start: 0.8147 (t0) cc_final: 0.7859 (t0) REVERT: B 458 LYS cc_start: 0.9229 (mttt) cc_final: 0.8939 (mtpp) REVERT: B 646 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7928 (ttp80) REVERT: B 760 CYS cc_start: 0.5879 (OUTLIER) cc_final: 0.5627 (t) REVERT: B 900 MET cc_start: 0.8208 (mtp) cc_final: 0.7915 (mtp) REVERT: B 1037 SER cc_start: 0.9171 (t) cc_final: 0.8782 (m) REVERT: B 1043 CYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7980 (m) REVERT: B 1142 GLN cc_start: 0.8186 (tp40) cc_final: 0.7964 (tp40) REVERT: C 19 THR cc_start: 0.8364 (p) cc_final: 0.8098 (t) REVERT: C 111 ASP cc_start: 0.8142 (t0) cc_final: 0.7594 (t0) REVERT: C 332 ILE cc_start: 0.9193 (mm) cc_final: 0.8965 (mp) REVERT: C 458 LYS cc_start: 0.9194 (mttt) cc_final: 0.8871 (mtpp) REVERT: C 483 VAL cc_start: 0.8542 (t) cc_final: 0.8301 (p) REVERT: C 571 ASP cc_start: 0.8924 (t0) cc_final: 0.8613 (t0) REVERT: C 740 MET cc_start: 0.8954 (mmm) cc_final: 0.8526 (mtp) REVERT: C 760 CYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5853 (t) REVERT: C 823 PHE cc_start: 0.8002 (t80) cc_final: 0.7615 (t80) REVERT: C 1037 SER cc_start: 0.9334 (t) cc_final: 0.8886 (m) outliers start: 64 outliers final: 52 residues processed: 212 average time/residue: 0.1714 time to fit residues: 61.1872 Evaluate side-chains 201 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 144 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR 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 212 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 222 optimal weight: 0.0060 chunk 293 optimal weight: 2.9990 chunk 286 optimal weight: 0.0040 chunk 137 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 overall best weight: 0.7010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 955 ASN C 606 ASN C 913 GLN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.111436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091091 restraints weight = 45595.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094704 restraints weight = 22611.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.097094 restraints weight = 14458.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098650 restraints weight = 10699.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.099599 restraints weight = 8700.437| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28200 Z= 0.123 Angle : 0.550 8.930 38511 Z= 0.277 Chirality : 0.044 0.332 4563 Planarity : 0.003 0.056 4815 Dihedral : 6.634 61.153 3777 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.01 % Allowed : 9.82 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3309 helix: 2.07 (0.20), residues: 720 sheet: 0.36 (0.19), residues: 729 loop : -0.48 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 847 TYR 0.022 0.001 TYR C 248 PHE 0.022 0.001 PHE B 823 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (28062) covalent geometry : angle 0.52021 / 0.27 (38142) SS BOND : bond 0.00213 / 0.14 ( 45) SS BOND : angle 0.93068 / 0.68 ( 90) hydrogen bonds : bond 0.04036 / 2.73 ( 1078) hydrogen bonds : angle 5.06992 / 3.56 ( 3072) link_BETA1-4 : bond 0.00417 / 0.27 ( 45) link_BETA1-4 : angle 2.06838 / 1.36 ( 135) link_NAG-ASN : bond 0.00276 / 0.19 ( 48) link_NAG-ASN : angle 2.13804 / 1.52 ( 144) ********************** 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 209 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 151 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8359 (p) cc_final: 0.8095 (t) REVERT: A 572 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8573 (p) REVERT: A 737 ASP cc_start: 0.8237 (t0) cc_final: 0.7900 (t0) REVERT: A 1037 SER cc_start: 0.9314 (t) cc_final: 0.8955 (m) REVERT: B 19 THR cc_start: 0.8565 (p) cc_final: 0.8275 (t) REVERT: B 111 ASP cc_start: 0.8171 (t0) cc_final: 0.7879 (t0) REVERT: B 458 LYS cc_start: 0.9237 (mttt) cc_final: 0.8945 (mtpp) REVERT: B 646 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7965 (ttp80) REVERT: B 760 CYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5647 (t) REVERT: B 900 MET cc_start: 0.8390 (mtp) cc_final: 0.8078 (mtp) REVERT: B 960 ASN cc_start: 0.8629 (m-40) cc_final: 0.8356 (m110) REVERT: B 1037 SER cc_start: 0.9160 (t) cc_final: 0.8720 (m) REVERT: B 1043 CYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7980 (m) REVERT: B 1142 GLN cc_start: 0.8281 (tp40) cc_final: 0.8080 (tp40) REVERT: C 19 THR cc_start: 0.8358 (p) cc_final: 0.8094 (t) REVERT: C 111 ASP cc_start: 0.8130 (t0) cc_final: 0.7587 (t0) REVERT: C 332 ILE cc_start: 0.9194 (mm) cc_final: 0.8970 (mp) REVERT: C 458 LYS cc_start: 0.9197 (mttt) cc_final: 0.8871 (mtpp) REVERT: C 483 VAL cc_start: 0.8544 (t) cc_final: 0.8303 (p) REVERT: C 661 GLU cc_start: 0.8558 (tp30) cc_final: 0.8277 (tp30) REVERT: C 740 MET cc_start: 0.8955 (mmm) cc_final: 0.8525 (mtp) REVERT: C 760 CYS cc_start: 0.6134 (OUTLIER) cc_final: 0.5891 (t) REVERT: C 1037 SER cc_start: 0.9345 (OUTLIER) cc_final: 0.8886 (m) outliers start: 58 outliers final: 50 residues processed: 202 average time/residue: 0.1759 time to fit residues: 59.2718 Evaluate side-chains 201 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1042 PHE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1042 PHE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR 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 234 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 222 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 308 optimal weight: 0.0020 chunk 130 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 321 optimal weight: 2.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B 955 ASN C 606 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.111334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.091019 restraints weight = 45322.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.094623 restraints weight = 22491.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.096912 restraints weight = 14394.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098509 restraints weight = 10745.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099532 restraints weight = 8731.864| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28200 Z= 0.125 Angle : 0.546 8.862 38511 Z= 0.276 Chirality : 0.044 0.332 4563 Planarity : 0.003 0.056 4815 Dihedral : 6.542 60.480 3777 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.01 % Allowed : 9.79 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3309 helix: 2.23 (0.20), residues: 702 sheet: 0.30 (0.19), residues: 744 loop : -0.46 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1107 TYR 0.022 0.001 TYR C 248 PHE 0.022 0.001 PHE B 823 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (28062) covalent geometry : angle 0.51665 / 0.27 (38142) SS BOND : bond 0.00218 / 0.15 ( 45) SS BOND : angle 0.93298 / 0.68 ( 90) hydrogen bonds : bond 0.04028 / 2.73 ( 1078) hydrogen bonds : angle 5.05149 / 3.55 ( 3072) link_BETA1-4 : bond 0.00416 / 0.27 ( 45) link_BETA1-4 : angle 2.05306 / 1.35 ( 135) link_NAG-ASN : bond 0.00272 / 0.18 ( 48) link_NAG-ASN : angle 2.12863 / 1.51 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4168.15 seconds wall clock time: 73 minutes 20.00 seconds (4400.00 seconds total)