Starting phenix.real_space_refine on Mon Jul 6 21:14:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y1z_33576/07_2026/7y1z_33576.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1z_33576/07_2026/7y1z_33576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y1z_33576/07_2026/7y1z_33576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1z_33576/07_2026/7y1z_33576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y1z_33576/07_2026/7y1z_33576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1z_33576/07_2026/7y1z_33576.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y1z_33576/07_2026/7y1z_33576.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y1z_33576/07_2026/7y1z_33576.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.082 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 195 5.16 5 C 25240 2.51 5 N 6435 2.21 5 O 7713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39583 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 7843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7843 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "B" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7837 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7837 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "F" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "H" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} 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: "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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.08, per 1000 atoms: 0.20 Number of scatterers: 39583 At special positions: 0 Unit cell: (184.79, 195.66, 247.836, 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 195 16.00 O 7713 8.00 N 6435 7.00 C 25240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.09 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.94 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.41 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=1.88 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.18 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.07 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.14 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.09 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.95 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.94 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.06 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.09 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.98 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=1.89 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.91 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.06 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.08 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.20 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.04 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.04 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 701 " - " ASN D 322 " " NAG E 1 " - " ASN A 331 " " NAG F 701 " - " ASN F 322 " " NAG G 1 " - " ASN A 343 " " NAG H 701 " - " ASN H 322 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN D 53 " " NAG e 1 " - " ASN D 90 " " NAG f 1 " - " ASN D 103 " " NAG g 1 " - " ASN D 432 " " NAG h 1 " - " ASN D 546 " " NAG i 1 " - " ASN F 53 " " NAG j 1 " - " ASN F 90 " " NAG k 1 " - " ASN F 103 " " NAG l 1 " - " ASN F 432 " " NAG m 1 " - " ASN F 546 " " NAG n 1 " - " ASN H 53 " " NAG o 1 " - " ASN H 90 " " NAG p 1 " - " ASN H 103 " " NAG q 1 " - " ASN H 432 " " NAG r 1 " - " ASN H 546 " Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9014 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 49 sheets defined 39.4% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.708A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.681A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.018A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.693A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.529A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.791A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.701A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.703A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.983A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.679A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.018A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.693A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.516A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.650A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.680A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.018A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.693A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 933 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.321A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.810A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 22 through 53 removed outlier: 4.096A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 81 removed outlier: 4.154A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 192 removed outlier: 3.910A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.190A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.733A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.084A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 281 removed outlier: 4.178A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.785A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.728A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.653A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.691A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.564A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.607A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 531 removed outlier: 4.535A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.973A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix removed outlier: 3.599A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 53 removed outlier: 4.096A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.155A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 157 through 192 removed outlier: 3.909A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 4.189A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 252 removed outlier: 3.731A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.084A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR F 252 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 281 removed outlier: 4.178A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.785A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.729A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.652A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.691A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.563A pdb=" N ILE F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 420 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 448 through 466 removed outlier: 4.607A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 531 removed outlier: 4.534A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.973A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 598 Proline residue: F 590 - end of helix removed outlier: 3.599A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 53 removed outlier: 4.096A pdb=" N LYS H 31 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 removed outlier: 4.154A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN H 64 " --> pdb=" O GLN H 60 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA H 65 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 155 Processing helix chain 'H' and resid 157 through 192 removed outlier: 3.909A pdb=" N TRP H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG H 169 " --> pdb=" O TRP H 165 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU H 176 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG H 177 " --> pdb=" O GLY H 173 " (cutoff:3.500A) Proline residue: H 178 - end of helix removed outlier: 4.189A pdb=" N GLU H 182 " --> pdb=" O PRO H 178 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL H 185 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 205 Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 220 through 252 removed outlier: 3.731A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU H 232 " --> pdb=" O HIS H 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE H 233 " --> pdb=" O THR H 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS H 234 " --> pdb=" O PHE H 230 " (cutoff:3.500A) Proline residue: H 235 - end of helix removed outlier: 4.083A pdb=" N HIS H 239 " --> pdb=" O PRO H 235 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA H 251 " --> pdb=" O LYS H 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR H 252 " --> pdb=" O LEU H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 267 No H-bonds generated for 'chain 'H' and resid 265 through 267' Processing helix chain 'H' and resid 275 through 281 removed outlier: 4.179A pdb=" N SER H 280 " --> pdb=" O ASN H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.785A pdb=" N VAL H 298 " --> pdb=" O THR H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 319 removed outlier: 3.728A pdb=" N ILE H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE H 308 " --> pdb=" O ALA H 304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL H 318 " --> pdb=" O PHE H 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY H 319 " --> pdb=" O PHE H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.652A pdb=" N ASN H 330 " --> pdb=" O GLY H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 385 removed outlier: 3.691A pdb=" N HIS H 373 " --> pdb=" O PHE H 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS H 378 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR H 385 " --> pdb=" O TYR H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 393 Processing helix chain 'H' and resid 399 through 413 removed outlier: 3.564A pdb=" N ILE H 407 " --> pdb=" O ALA H 403 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 420 Processing helix chain 'H' and resid 431 through 444 Processing helix chain 'H' and resid 448 through 466 removed outlier: 4.606A pdb=" N PHE H 452 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 Processing helix chain 'H' and resid 499 through 502 Processing helix chain 'H' and resid 503 through 508 Processing helix chain 'H' and resid 513 through 531 removed outlier: 4.534A pdb=" N THR H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE H 523 " --> pdb=" O THR H 519 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 542 Processing helix chain 'H' and resid 548 through 559 removed outlier: 3.973A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG H 559 " --> pdb=" O PHE H 555 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU H 571 " --> pdb=" O THR H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 598 Proline residue: H 590 - end of helix removed outlier: 3.599A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.685A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.740A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.333A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.613A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.797A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.811A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.076A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.484A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.770A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.850A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.686A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 7.497A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.925A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.329A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 323 through 328 removed outlier: 5.612A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.796A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.811A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 659 through 660 removed outlier: 4.530A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.473A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.546A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.943A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.686A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 49 through 55 removed outlier: 7.499A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.740A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.049A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.560A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.796A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.811A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.301A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AF1, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF3, first strand: chain 'H' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU H 262 " --> pdb=" O VAL H 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'H' and resid 347 through 350 1564 hydrogen bonds defined for protein. 4386 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: 9.18 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8630 1.33 - 1.45: 10902 1.45 - 1.58: 20726 1.58 - 1.71: 0 1.71 - 1.83: 285 Bond restraints: 40543 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.080 1.20e-02 6.94e+03 4.40e+01 bond pdb=" C THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.34e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.33e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.33e+01 bond pdb=" N PRO A1143 " pdb=" CD PRO A1143 " ideal model delta sigma weight residual 1.473 1.412 0.061 1.40e-02 5.10e+03 1.92e+01 ... (remaining 40538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 54168 2.70 - 5.41: 837 5.41 - 8.11: 80 8.11 - 10.81: 23 10.81 - 13.52: 6 Bond angle restraints: 55114 Sorted by residual: angle pdb=" N PHE H 28 " pdb=" CA PHE H 28 " pdb=" C PHE H 28 " ideal model delta sigma weight residual 111.24 101.82 9.42 1.29e+00 6.01e-01 5.34e+01 angle pdb=" N PHE F 28 " pdb=" CA PHE F 28 " pdb=" C PHE F 28 " ideal model delta sigma weight residual 111.24 101.84 9.40 1.29e+00 6.01e-01 5.31e+01 angle pdb=" N PHE D 28 " pdb=" CA PHE D 28 " pdb=" C PHE D 28 " ideal model delta sigma weight residual 111.24 101.85 9.39 1.29e+00 6.01e-01 5.29e+01 angle pdb=" N LEU F 45 " pdb=" CA LEU F 45 " pdb=" C LEU F 45 " ideal model delta sigma weight residual 111.07 103.93 7.14 1.07e+00 8.73e-01 4.46e+01 angle pdb=" N LEU D 45 " pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 111.07 103.95 7.12 1.07e+00 8.73e-01 4.43e+01 ... (remaining 55109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 21328 17.88 - 35.77: 1467 35.77 - 53.65: 319 53.65 - 71.54: 78 71.54 - 89.42: 65 Dihedral angle restraints: 23257 sinusoidal: 9268 harmonic: 13989 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 3.42 -89.42 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 25.65 67.35 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 23254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 6339 0.331 - 0.661: 7 0.661 - 0.992: 5 0.992 - 1.323: 0 1.323 - 1.653: 2 Chirality restraints: 6353 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.04e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.02e+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 -1.95 -0.45 2.00e-02 2.50e+03 5.00e+02 ... (remaining 6350 not shown) Planarity restraints: 7050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.239 2.00e-02 2.50e+03 3.35e-01 1.40e+03 pdb=" CG ASN B 331 " -0.113 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.563 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " 0.418 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.142 2.00e-02 2.50e+03 1.63e-01 3.34e+02 pdb=" CG ASN A 801 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.271 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.105 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" CG ASN A 331 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.196 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.140 2.00e-02 2.50e+03 ... (remaining 7047 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 233 2.52 - 3.12: 30471 3.12 - 3.71: 55966 3.71 - 4.31: 81226 4.31 - 4.90: 133628 Nonbonded interactions: 301524 Sorted by model distance: nonbonded pdb=" O ARG A 328 " pdb=" CD1 PHE A 329 " model vdw 1.926 3.340 nonbonded pdb=" O ASP B 40 " pdb=" O LYS B 41 " model vdw 1.995 3.040 nonbonded pdb=" O VAL C 445 " pdb=" OG SER C 446 " model vdw 2.034 3.040 nonbonded pdb=" O VAL B 445 " pdb=" OG SER B 446 " model vdw 2.035 3.040 nonbonded pdb=" O VAL A 445 " pdb=" OG SER A 446 " model vdw 2.035 3.040 ... (remaining 301519 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1408)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.500 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5249 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 : 0.008 0.376 40695 Z= 0.459 Angle : 1.124 61.444 55522 Z= 0.606 Chirality : 0.069 1.653 6353 Planarity : 0.005 0.106 6984 Dihedral : 13.599 88.438 14099 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 1.65 % Allowed : 6.76 % Favored : 91.59 % Rotamer: Outliers : 1.54 % Allowed : 4.72 % Favored : 93.73 % Cbeta Deviations : 0.02 % 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: -3.20 (0.11), residues: 4720 helix: -1.64 (0.11), residues: 1645 sheet: -1.15 (0.19), residues: 649 loop : -2.81 (0.11), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 161 TYR 0.014 0.001 TYR C 369 PHE 0.013 0.001 PHE C 456 TRP 0.013 0.001 TRP H 594 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.43 (40543) covalent geometry : angle 0.89175 / 0.54 (55114) SS BOND : bond 0.09061 / 4.62 ( 48) SS BOND : angle 12.07086 / 7.10 ( 96) hydrogen bonds : bond 0.20043 / 12.91 ( 1535) hydrogen bonds : angle 7.87873 / 5.29 ( 4386) link_BETA1-4 : bond 0.00890 / 0.46 ( 38) link_BETA1-4 : angle 4.96467 / 3.30 ( 114) link_NAG-ASN : bond 0.03892 / 2.52 ( 66) link_NAG-ASN : angle 6.94588 / 4.73 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 777 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.5924 (m-80) cc_final: 0.5619 (m-80) REVERT: A 332 ILE cc_start: 0.3761 (OUTLIER) cc_final: 0.3325 (tt) REVERT: A 371 PHE cc_start: 0.0628 (OUTLIER) cc_final: 0.0053 (t80) REVERT: A 800 PHE cc_start: 0.6115 (m-80) cc_final: 0.5049 (m-80) REVERT: B 909 ILE cc_start: 0.7729 (pt) cc_final: 0.7195 (pt) REVERT: B 1143 PRO cc_start: 0.8092 (Cg_endo) cc_final: 0.7459 (Cg_exo) REVERT: C 1031 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6992 (tt0) REVERT: D 85 LEU cc_start: -0.1612 (tp) cc_final: -0.1826 (pt) REVERT: D 189 GLU cc_start: 0.4969 (mt-10) cc_final: 0.4574 (mm-30) REVERT: D 221 GLN cc_start: 0.3678 (tt0) cc_final: 0.3295 (mm-40) REVERT: F 31 LYS cc_start: 0.0371 (OUTLIER) cc_final: 0.0159 (tptt) REVERT: F 474 MET cc_start: -0.2123 (mmp) cc_final: -0.2789 (ttt) REVERT: H 39 LEU cc_start: 0.4931 (OUTLIER) cc_final: 0.4672 (mt) REVERT: H 270 MET cc_start: 0.2103 (tpt) cc_final: 0.1050 (tpp) outliers start: 65 outliers final: 17 residues processed: 831 average time/residue: 0.2254 time to fit residues: 306.3532 Evaluate side-chains 378 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 357 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain H residue 39 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 314 GLN A 417 ASN A 422 ASN A 690 GLN B 30 ASN B 271 GLN B 314 GLN B 334 ASN B 417 ASN B 450 ASN B 506 GLN B 901 GLN C 121 ASN C 417 ASN C 755 GLN C 762 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS D 24 GLN D 101 GLN D 137 ASN D 210 ASN D 374 HIS D 472 GLN D 599 ASN F 24 GLN F 101 GLN F 137 ASN F 277 ASN F 374 HIS F 417 HIS F 442 GLN F 472 GLN F 599 ASN H 24 GLN ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN H 277 ASN H 373 HIS H 417 HIS H 472 GLN H 580 ASN H 599 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.257766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.211674 restraints weight = 60257.952| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 3.59 r_work: 0.3534 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.107 40695 Z= 0.375 Angle : 0.985 20.250 55522 Z= 0.483 Chirality : 0.056 0.380 6353 Planarity : 0.006 0.087 6984 Dihedral : 6.261 57.041 5191 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.31 % Favored : 93.22 % Rotamer: Outliers : 2.71 % Allowed : 11.11 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.11), residues: 4720 helix: -0.84 (0.12), residues: 1675 sheet: -1.48 (0.18), residues: 699 loop : -2.64 (0.11), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 493 TYR 0.036 0.003 TYR B 501 PHE 0.034 0.003 PHE A1052 TRP 0.050 0.002 TRP F 461 HIS 0.016 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00913 / 0.37 (40543) covalent geometry : angle 0.93420 / 0.47 (55114) SS BOND : bond 0.00653 / 0.36 ( 48) SS BOND : angle 3.02434 / 1.90 ( 96) hydrogen bonds : bond 0.06754 / 4.42 ( 1535) hydrogen bonds : angle 5.72554 / 3.85 ( 4386) link_BETA1-4 : bond 0.01361 / 0.75 ( 38) link_BETA1-4 : angle 2.89783 / 2.02 ( 114) link_NAG-ASN : bond 0.01122 / 0.59 ( 66) link_NAG-ASN : angle 4.45915 / 2.77 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 378 time to evaluate : 1.416 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 205 SER cc_start: 0.8616 (p) cc_final: 0.8386 (p) REVERT: A 523 THR cc_start: 0.1941 (OUTLIER) cc_final: 0.1704 (m) REVERT: A 756 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.5829 (t80) REVERT: A 855 PHE cc_start: 0.6433 (t80) cc_final: 0.5081 (m-80) REVERT: A 1111 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8092 (pp20) REVERT: B 200 TYR cc_start: 0.6680 (m-10) cc_final: 0.6466 (m-10) REVERT: B 276 LEU cc_start: 0.8396 (tp) cc_final: 0.8133 (pt) REVERT: B 523 THR cc_start: 0.5091 (OUTLIER) cc_final: 0.4861 (m) REVERT: B 568 ASP cc_start: 0.7072 (p0) cc_final: 0.6869 (p0) REVERT: B 658 ASN cc_start: 0.7401 (t0) cc_final: 0.7187 (m-40) REVERT: C 121 ASN cc_start: 0.6238 (OUTLIER) cc_final: 0.5972 (p0) REVERT: C 200 TYR cc_start: 0.7256 (m-80) cc_final: 0.7037 (m-80) REVERT: C 266 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: C 307 THR cc_start: 0.8949 (m) cc_final: 0.8648 (p) REVERT: C 917 TYR cc_start: 0.8648 (m-80) cc_final: 0.8303 (m-80) REVERT: C 1002 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7575 (tp-100) REVERT: D 85 LEU cc_start: -0.0376 (tp) cc_final: -0.0811 (pt) REVERT: D 189 GLU cc_start: 0.5499 (mt-10) cc_final: 0.5169 (mm-30) REVERT: D 190 MET cc_start: -0.1457 (tmm) cc_final: -0.2202 (ttp) REVERT: D 213 ASP cc_start: 0.2261 (t0) cc_final: 0.1441 (m-30) REVERT: D 455 MET cc_start: 0.0891 (tmm) cc_final: 0.0350 (ttp) REVERT: F 150 GLU cc_start: 0.2714 (tm-30) cc_final: 0.1617 (mm-30) REVERT: F 152 MET cc_start: 0.0865 (mmt) cc_final: 0.0269 (mmp) REVERT: F 474 MET cc_start: -0.1628 (mmp) cc_final: -0.3166 (ttt) REVERT: H 39 LEU cc_start: 0.4241 (OUTLIER) cc_final: 0.3909 (mt) REVERT: H 82 MET cc_start: 0.3182 (mtp) cc_final: 0.2685 (mpp) REVERT: H 270 MET cc_start: 0.0408 (tpt) cc_final: 0.0074 (mmm) REVERT: H 383 MET cc_start: 0.0871 (mtp) cc_final: -0.0004 (tmm) outliers start: 114 outliers final: 52 residues processed: 475 average time/residue: 0.2145 time to fit residues: 174.6379 Evaluate side-chains 334 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1057 PRO Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 563 SER Chi-restraints excluded: chain H residue 580 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 223 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 155 optimal weight: 0.0470 chunk 124 optimal weight: 20.0000 chunk 280 optimal weight: 10.0000 chunk 433 optimal weight: 40.0000 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 450 ASN A 955 ASN B 87 ASN B 207 HIS B1005 GLN D 34 HIS D 101 GLN D 417 HIS ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS F 429 GLN ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.261141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.212469 restraints weight = 60478.455| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 3.97 r_work: 0.3541 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 40695 Z= 0.135 Angle : 0.714 17.944 55522 Z= 0.344 Chirality : 0.046 0.489 6353 Planarity : 0.004 0.095 6984 Dihedral : 5.147 54.335 5150 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.36 % Favored : 94.34 % Rotamer: Outliers : 2.18 % Allowed : 13.01 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.11), residues: 4720 helix: -0.09 (0.13), residues: 1696 sheet: -1.11 (0.18), residues: 715 loop : -2.29 (0.11), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 460 TYR 0.022 0.001 TYR A 453 PHE 0.021 0.001 PHE H 285 TRP 0.014 0.001 TRP D 459 HIS 0.007 0.001 HIS H 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (40543) covalent geometry : angle 0.66721 / 0.33 (55114) SS BOND : bond 0.00519 / 0.37 ( 48) SS BOND : angle 2.54574 / 1.74 ( 96) hydrogen bonds : bond 0.04830 / 3.14 ( 1535) hydrogen bonds : angle 5.15303 / 3.48 ( 4386) link_BETA1-4 : bond 0.00704 / 0.39 ( 38) link_BETA1-4 : angle 2.37717 / 1.70 ( 114) link_NAG-ASN : bond 0.00580 / 0.38 ( 66) link_NAG-ASN : angle 3.54946 / 2.18 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 313 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.1950 (OUTLIER) cc_final: 0.1698 (m) REVERT: A 754 LEU cc_start: 0.7445 (tp) cc_final: 0.7114 (mp) REVERT: A 756 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.5714 (t80) REVERT: A 767 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7845 (mm) REVERT: A 1010 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6141 (tp40) REVERT: B 276 LEU cc_start: 0.8447 (tp) cc_final: 0.7985 (pt) REVERT: B 568 ASP cc_start: 0.7050 (p0) cc_final: 0.6828 (p0) REVERT: B 658 ASN cc_start: 0.7200 (t0) cc_final: 0.6948 (m110) REVERT: C 200 TYR cc_start: 0.7578 (m-80) cc_final: 0.7280 (m-80) REVERT: C 307 THR cc_start: 0.8952 (m) cc_final: 0.8702 (p) REVERT: C 859 THR cc_start: 0.8102 (m) cc_final: 0.7500 (p) REVERT: D 168 TRP cc_start: -0.1964 (t-100) cc_final: -0.2382 (t-100) REVERT: D 190 MET cc_start: -0.1606 (tmm) cc_final: -0.2327 (ttp) REVERT: D 213 ASP cc_start: 0.1985 (t0) cc_final: 0.1260 (m-30) REVERT: D 438 PHE cc_start: 0.0701 (t80) cc_final: -0.1074 (m-80) REVERT: D 455 MET cc_start: 0.1339 (tmm) cc_final: 0.0868 (ttp) REVERT: F 150 GLU cc_start: 0.2404 (tm-30) cc_final: 0.1254 (mm-30) REVERT: F 154 ASN cc_start: 0.1496 (m-40) cc_final: 0.1119 (t0) REVERT: F 323 MET cc_start: -0.1765 (mmt) cc_final: -0.1992 (tpt) REVERT: H 39 LEU cc_start: 0.4360 (OUTLIER) cc_final: 0.3991 (mt) REVERT: H 141 CYS cc_start: -0.0219 (OUTLIER) cc_final: -0.0502 (p) REVERT: H 383 MET cc_start: 0.0691 (mtp) cc_final: -0.0052 (tmm) REVERT: H 587 TYR cc_start: 0.2308 (OUTLIER) cc_final: 0.1917 (m-80) outliers start: 92 outliers final: 38 residues processed: 383 average time/residue: 0.2117 time to fit residues: 140.3244 Evaluate side-chains 306 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 542 CYS Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 469 optimal weight: 30.0000 chunk 166 optimal weight: 0.0370 chunk 439 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 336 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 312 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 chunk 432 optimal weight: 40.0000 chunk 254 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 2.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 644 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 755 GLN C 762 GLN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 HIS H 373 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.257063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.206606 restraints weight = 60041.202| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 4.04 r_work: 0.3501 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 40695 Z= 0.203 Angle : 0.736 11.685 55522 Z= 0.357 Chirality : 0.048 0.480 6353 Planarity : 0.005 0.065 6984 Dihedral : 4.960 53.130 5142 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 2.49 % Allowed : 13.81 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.12), residues: 4720 helix: 0.18 (0.13), residues: 1694 sheet: -1.14 (0.18), residues: 744 loop : -2.21 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 319 TYR 0.022 0.002 TYR B 660 PHE 0.031 0.002 PHE A 855 TRP 0.022 0.001 TRP D 203 HIS 0.008 0.001 HIS F 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (40543) covalent geometry : angle 0.70193 / 0.35 (55114) SS BOND : bond 0.00556 / 0.37 ( 48) SS BOND : angle 2.20600 / 1.47 ( 96) hydrogen bonds : bond 0.04937 / 3.20 ( 1535) hydrogen bonds : angle 5.02316 / 3.39 ( 4386) link_BETA1-4 : bond 0.00659 / 0.37 ( 38) link_BETA1-4 : angle 2.24034 / 1.61 ( 114) link_NAG-ASN : bond 0.00535 / 0.30 ( 66) link_NAG-ASN : angle 3.05343 / 1.88 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 297 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.8214 (m-10) cc_final: 0.7970 (m-10) REVERT: A 767 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.7936 (mm) REVERT: A 1010 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6255 (tp40) REVERT: C 200 TYR cc_start: 0.7813 (m-80) cc_final: 0.7489 (m-80) REVERT: C 307 THR cc_start: 0.9064 (m) cc_final: 0.8791 (p) REVERT: C 1002 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7340 (tp-100) REVERT: D 168 TRP cc_start: -0.1954 (t-100) cc_final: -0.2223 (t-100) REVERT: D 189 GLU cc_start: 0.5277 (pt0) cc_final: 0.4878 (mm-30) REVERT: D 190 MET cc_start: -0.1301 (tmm) cc_final: -0.1692 (ttp) REVERT: D 213 ASP cc_start: 0.1900 (t0) cc_final: 0.1155 (m-30) REVERT: D 294 THR cc_start: 0.2198 (p) cc_final: 0.1890 (t) REVERT: D 383 MET cc_start: 0.4201 (ptp) cc_final: 0.2894 (ppp) REVERT: D 438 PHE cc_start: 0.0786 (t80) cc_final: -0.0921 (m-80) REVERT: D 480 MET cc_start: -0.0835 (mtm) cc_final: -0.1077 (mtt) REVERT: F 150 GLU cc_start: 0.2244 (tm-30) cc_final: 0.1495 (mm-30) REVERT: F 293 VAL cc_start: 0.0492 (OUTLIER) cc_final: -0.0053 (t) REVERT: F 351 LEU cc_start: 0.0525 (OUTLIER) cc_final: 0.0161 (mp) REVERT: H 165 TRP cc_start: 0.1716 (t60) cc_final: 0.0896 (t60) REVERT: H 383 MET cc_start: 0.0686 (mtp) cc_final: -0.0035 (tmm) REVERT: H 587 TYR cc_start: 0.2547 (OUTLIER) cc_final: 0.2178 (m-80) outliers start: 105 outliers final: 60 residues processed: 385 average time/residue: 0.1897 time to fit residues: 128.3113 Evaluate side-chains 308 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 243 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 83 optimal weight: 6.9990 chunk 371 optimal weight: 50.0000 chunk 179 optimal weight: 0.9980 chunk 332 optimal weight: 10.0000 chunk 471 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 chunk 330 optimal weight: 40.0000 chunk 361 optimal weight: 50.0000 chunk 367 optimal weight: 0.0170 chunk 129 optimal weight: 20.0000 chunk 341 optimal weight: 50.0000 overall best weight: 3.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN B 207 HIS C 121 ASN C1005 GLN D 265 HIS D 340 GLN F 154 ASN ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.253579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.203955 restraints weight = 61315.177| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 4.13 r_work: 0.3404 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 40695 Z= 0.249 Angle : 0.767 18.240 55522 Z= 0.369 Chirality : 0.050 0.740 6353 Planarity : 0.005 0.070 6984 Dihedral : 4.986 59.602 5140 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.89 % Favored : 93.83 % Rotamer: Outliers : 3.23 % Allowed : 14.38 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.12), residues: 4720 helix: 0.22 (0.13), residues: 1694 sheet: -1.17 (0.18), residues: 747 loop : -2.16 (0.12), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 983 TYR 0.022 0.002 TYR C1067 PHE 0.029 0.002 PHE A 855 TRP 0.017 0.001 TRP D 478 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.25 (40543) covalent geometry : angle 0.73203 / 0.36 (55114) SS BOND : bond 0.00641 / 0.43 ( 48) SS BOND : angle 2.31888 / 1.54 ( 96) hydrogen bonds : bond 0.05027 / 3.27 ( 1535) hydrogen bonds : angle 5.07164 / 3.43 ( 4386) link_BETA1-4 : bond 0.00971 / 0.51 ( 38) link_BETA1-4 : angle 2.25395 / 1.62 ( 114) link_NAG-ASN : bond 0.00598 / 0.36 ( 66) link_NAG-ASN : angle 3.21765 / 1.95 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 274 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.8165 (m-80) cc_final: 0.7806 (m-80) REVERT: A 559 PHE cc_start: 0.8726 (m-10) cc_final: 0.8515 (m-10) REVERT: A 574 ASP cc_start: 0.7866 (p0) cc_final: 0.7617 (p0) REVERT: A 699 LEU cc_start: 0.7329 (pp) cc_final: 0.7122 (pp) REVERT: A 754 LEU cc_start: 0.8651 (tp) cc_final: 0.8259 (mp) REVERT: A 767 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8080 (mm) REVERT: A 1010 GLN cc_start: 0.7038 (OUTLIER) cc_final: 0.6226 (tp40) REVERT: B 281 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8421 (pt0) REVERT: B 856 ASN cc_start: 0.8160 (m110) cc_final: 0.7952 (p0) REVERT: B 900 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8101 (mtp) REVERT: C 121 ASN cc_start: 0.6623 (OUTLIER) cc_final: 0.6322 (p0) REVERT: C 200 TYR cc_start: 0.7985 (m-80) cc_final: 0.7696 (m-80) REVERT: C 917 TYR cc_start: 0.8759 (m-80) cc_final: 0.8518 (m-80) REVERT: C 1002 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7407 (tp-100) REVERT: D 189 GLU cc_start: 0.5069 (pt0) cc_final: 0.4750 (mm-30) REVERT: D 190 MET cc_start: -0.0926 (tmm) cc_final: -0.1442 (ttp) REVERT: D 213 ASP cc_start: 0.1867 (t0) cc_final: 0.1187 (m-30) REVERT: D 294 THR cc_start: 0.2496 (p) cc_final: 0.2255 (t) REVERT: D 438 PHE cc_start: 0.0903 (t80) cc_final: -0.0858 (m-80) REVERT: D 474 MET cc_start: 0.2096 (mpp) cc_final: 0.1410 (mtt) REVERT: D 571 GLU cc_start: 0.2477 (OUTLIER) cc_final: 0.2219 (pt0) REVERT: F 323 MET cc_start: -0.2069 (tpt) cc_final: -0.2889 (ppp) REVERT: F 351 LEU cc_start: 0.0910 (OUTLIER) cc_final: 0.0513 (mp) REVERT: F 366 MET cc_start: 0.0990 (mmm) cc_final: 0.0714 (mmm) REVERT: F 587 TYR cc_start: -0.0708 (OUTLIER) cc_final: -0.1197 (m-10) REVERT: H 383 MET cc_start: 0.0362 (mtp) cc_final: -0.0212 (tmm) REVERT: H 587 TYR cc_start: 0.2695 (OUTLIER) cc_final: 0.2448 (m-80) outliers start: 136 outliers final: 85 residues processed: 382 average time/residue: 0.2012 time to fit residues: 132.9191 Evaluate side-chains 336 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 242 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 587 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 396 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 414 optimal weight: 50.0000 chunk 128 optimal weight: 0.0570 chunk 412 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 337 optimal weight: 40.0000 chunk 445 optimal weight: 10.0000 overall best weight: 1.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 207 HIS B 207 HIS B 506 GLN C 314 GLN F 241 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.257224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.209275 restraints weight = 61870.784| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 4.08 r_work: 0.3501 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 40695 Z= 0.136 Angle : 0.664 14.730 55522 Z= 0.317 Chirality : 0.046 0.794 6353 Planarity : 0.004 0.060 6984 Dihedral : 4.694 54.839 5140 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.13 % Favored : 94.62 % Rotamer: Outliers : 2.37 % Allowed : 15.86 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.12), residues: 4720 helix: 0.57 (0.13), residues: 1687 sheet: -0.98 (0.18), residues: 722 loop : -2.04 (0.12), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 983 TYR 0.021 0.001 TYR A 269 PHE 0.031 0.001 PHE A 855 TRP 0.012 0.001 TRP A 64 HIS 0.027 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (40543) covalent geometry : angle 0.62985 / 0.31 (55114) SS BOND : bond 0.00492 / 0.33 ( 48) SS BOND : angle 2.30742 / 1.54 ( 96) hydrogen bonds : bond 0.04188 / 2.71 ( 1535) hydrogen bonds : angle 4.84208 / 3.27 ( 4386) link_BETA1-4 : bond 0.00609 / 0.33 ( 38) link_BETA1-4 : angle 2.04372 / 1.47 ( 114) link_NAG-ASN : bond 0.00526 / 0.29 ( 66) link_NAG-ASN : angle 2.89701 / 1.80 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 263 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.8155 (m-80) cc_final: 0.7819 (m-80) REVERT: A 379 CYS cc_start: 0.2758 (OUTLIER) cc_final: 0.2116 (p) REVERT: A 559 PHE cc_start: 0.8659 (m-10) cc_final: 0.8458 (m-10) REVERT: A 574 ASP cc_start: 0.7640 (p0) cc_final: 0.7428 (p0) REVERT: A 754 LEU cc_start: 0.8717 (tp) cc_final: 0.8332 (mp) REVERT: A 767 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8096 (mm) REVERT: A 950 ASP cc_start: 0.8358 (m-30) cc_final: 0.8016 (m-30) REVERT: A 1010 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6059 (tp40) REVERT: C 1002 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7325 (tp40) REVERT: D 168 TRP cc_start: -0.1967 (t-100) cc_final: -0.2405 (t-100) REVERT: D 189 GLU cc_start: 0.5158 (pt0) cc_final: 0.4825 (mm-30) REVERT: D 190 MET cc_start: -0.0952 (tmm) cc_final: -0.1290 (ttp) REVERT: D 213 ASP cc_start: 0.1796 (t0) cc_final: 0.1100 (m-30) REVERT: D 294 THR cc_start: 0.2197 (p) cc_final: 0.1958 (t) REVERT: D 438 PHE cc_start: 0.0893 (t80) cc_final: -0.0671 (m-80) REVERT: D 474 MET cc_start: 0.2033 (mpp) cc_final: 0.1283 (mtp) REVERT: D 480 MET cc_start: -0.0826 (ptt) cc_final: -0.1322 (mtt) REVERT: D 502 SER cc_start: 0.2536 (OUTLIER) cc_final: 0.1677 (t) REVERT: D 559 ARG cc_start: 0.2370 (ptt90) cc_final: 0.1854 (tpt-90) REVERT: D 571 GLU cc_start: 0.2276 (OUTLIER) cc_final: 0.1945 (pt0) REVERT: F 323 MET cc_start: -0.1924 (tpt) cc_final: -0.2819 (ppp) REVERT: F 351 LEU cc_start: 0.1007 (OUTLIER) cc_final: 0.0542 (mp) REVERT: F 459 TRP cc_start: 0.0311 (t60) cc_final: -0.0333 (t60) REVERT: F 474 MET cc_start: -0.1547 (mmp) cc_final: -0.3267 (ttm) REVERT: F 587 TYR cc_start: -0.0747 (OUTLIER) cc_final: -0.1385 (m-10) REVERT: H 166 GLU cc_start: 0.3900 (tp30) cc_final: 0.3087 (tt0) REVERT: H 383 MET cc_start: 0.0220 (mtp) cc_final: -0.0247 (tmm) REVERT: H 587 TYR cc_start: 0.2666 (OUTLIER) cc_final: 0.2357 (m-80) outliers start: 100 outliers final: 65 residues processed: 344 average time/residue: 0.1924 time to fit residues: 116.1837 Evaluate side-chains 322 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 249 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 587 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 438 optimal weight: 0.1980 chunk 23 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 290 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 317 optimal weight: 30.0000 chunk 462 optimal weight: 9.9990 chunk 382 optimal weight: 10.0000 chunk 389 optimal weight: 40.0000 chunk 220 optimal weight: 0.9980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 207 HIS B 207 HIS B 422 ASN D 265 HIS F 505 HIS H 210 ASN H 442 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.256414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.207902 restraints weight = 61504.796| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 4.01 r_work: 0.3485 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.6476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 40695 Z= 0.154 Angle : 0.658 12.094 55522 Z= 0.314 Chirality : 0.046 0.495 6353 Planarity : 0.004 0.061 6984 Dihedral : 4.578 50.850 5140 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.55 % Favored : 94.19 % Rotamer: Outliers : 2.61 % Allowed : 15.83 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.12), residues: 4720 helix: 0.66 (0.13), residues: 1690 sheet: -0.92 (0.19), residues: 710 loop : -1.94 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.021 0.001 TYR C1067 PHE 0.021 0.001 PHE B 86 TRP 0.012 0.001 TRP A 64 HIS 0.008 0.001 HIS H 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (40543) covalent geometry : angle 0.62723 / 0.31 (55114) SS BOND : bond 0.00362 / 0.23 ( 48) SS BOND : angle 1.94594 / 1.28 ( 96) hydrogen bonds : bond 0.04176 / 2.70 ( 1535) hydrogen bonds : angle 4.80268 / 3.25 ( 4386) link_BETA1-4 : bond 0.00598 / 0.34 ( 38) link_BETA1-4 : angle 2.00388 / 1.45 ( 114) link_NAG-ASN : bond 0.00499 / 0.26 ( 66) link_NAG-ASN : angle 2.76034 / 1.72 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 264 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.8190 (m-80) cc_final: 0.7897 (m-80) REVERT: A 379 CYS cc_start: 0.2563 (OUTLIER) cc_final: 0.1678 (p) REVERT: A 574 ASP cc_start: 0.7460 (p0) cc_final: 0.7202 (p0) REVERT: A 754 LEU cc_start: 0.8786 (tp) cc_final: 0.8431 (mp) REVERT: A 767 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8067 (mm) REVERT: A 950 ASP cc_start: 0.8469 (m-30) cc_final: 0.8052 (m-30) REVERT: A 1010 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6018 (tp40) REVERT: B 926 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: C 105 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7770 (tt) REVERT: D 168 TRP cc_start: -0.2143 (t-100) cc_final: -0.2620 (t-100) REVERT: D 189 GLU cc_start: 0.5114 (pt0) cc_final: 0.4744 (mm-30) REVERT: D 190 MET cc_start: -0.0767 (tmm) cc_final: -0.1019 (ttp) REVERT: D 213 ASP cc_start: 0.1643 (t0) cc_final: 0.0962 (m-30) REVERT: D 294 THR cc_start: 0.2235 (p) cc_final: 0.2014 (t) REVERT: D 383 MET cc_start: 0.4274 (ptp) cc_final: 0.2828 (ppp) REVERT: D 438 PHE cc_start: 0.1063 (t80) cc_final: -0.0494 (m-80) REVERT: D 474 MET cc_start: 0.1966 (mpp) cc_final: 0.1694 (mmm) REVERT: D 480 MET cc_start: -0.0565 (ptt) cc_final: -0.1035 (mtt) REVERT: D 502 SER cc_start: 0.2478 (OUTLIER) cc_final: 0.1646 (t) REVERT: D 559 ARG cc_start: 0.2409 (ptt90) cc_final: 0.1869 (tpt-90) REVERT: D 571 GLU cc_start: 0.2246 (OUTLIER) cc_final: 0.1838 (pt0) REVERT: F 152 MET cc_start: 0.1007 (ptt) cc_final: 0.0420 (tpt) REVERT: F 323 MET cc_start: -0.1862 (tpt) cc_final: -0.2866 (ppp) REVERT: F 351 LEU cc_start: 0.1095 (OUTLIER) cc_final: 0.0629 (mp) REVERT: F 459 TRP cc_start: 0.0174 (t60) cc_final: -0.0383 (t60) REVERT: F 474 MET cc_start: -0.1540 (mmp) cc_final: -0.3219 (ttm) REVERT: F 502 SER cc_start: 0.3128 (OUTLIER) cc_final: 0.2894 (p) REVERT: F 587 TYR cc_start: -0.1076 (OUTLIER) cc_final: -0.1801 (m-10) REVERT: H 166 GLU cc_start: 0.3850 (tp30) cc_final: 0.3148 (tt0) REVERT: H 383 MET cc_start: 0.0126 (mtp) cc_final: -0.0336 (tmm) REVERT: H 468 ILE cc_start: -0.1462 (mt) cc_final: -0.1682 (mt) REVERT: H 587 TYR cc_start: 0.2649 (OUTLIER) cc_final: 0.2334 (m-80) outliers start: 110 outliers final: 71 residues processed: 354 average time/residue: 0.2003 time to fit residues: 123.3595 Evaluate side-chains 324 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 242 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain F residue 587 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 144 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 107 optimal weight: 40.0000 chunk 84 optimal weight: 0.9990 chunk 429 optimal weight: 8.9990 chunk 135 optimal weight: 40.0000 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 253 optimal weight: 2.9990 chunk 241 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 207 HIS B 207 HIS C 87 ASN F 505 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.257450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.209761 restraints weight = 61681.296| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 3.94 r_work: 0.3512 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40695 Z= 0.122 Angle : 0.632 10.874 55522 Z= 0.302 Chirality : 0.045 0.398 6353 Planarity : 0.004 0.056 6984 Dihedral : 4.423 51.198 5140 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.15 % Favored : 94.60 % Rotamer: Outliers : 2.23 % Allowed : 16.45 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.12), residues: 4720 helix: 0.85 (0.13), residues: 1695 sheet: -0.79 (0.19), residues: 712 loop : -1.85 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 983 TYR 0.020 0.001 TYR C1067 PHE 0.023 0.001 PHE A 86 TRP 0.015 0.001 TRP D 459 HIS 0.022 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (40543) covalent geometry : angle 0.60476 / 0.30 (55114) SS BOND : bond 0.00318 / 0.20 ( 48) SS BOND : angle 1.72310 / 1.15 ( 96) hydrogen bonds : bond 0.03802 / 2.46 ( 1535) hydrogen bonds : angle 4.69594 / 3.18 ( 4386) link_BETA1-4 : bond 0.00579 / 0.32 ( 38) link_BETA1-4 : angle 1.95469 / 1.42 ( 114) link_NAG-ASN : bond 0.00408 / 0.24 ( 66) link_NAG-ASN : angle 2.54074 / 1.58 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 246 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.8164 (m-80) cc_final: 0.7897 (m-80) REVERT: A 574 ASP cc_start: 0.7293 (p0) cc_final: 0.7071 (p0) REVERT: A 754 LEU cc_start: 0.8738 (tp) cc_final: 0.8523 (mp) REVERT: A 767 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8048 (mm) REVERT: A 950 ASP cc_start: 0.8326 (m-30) cc_final: 0.7913 (m-30) REVERT: A 1010 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.5973 (tp40) REVERT: B 926 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: C 895 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: C 975 SER cc_start: 0.7764 (p) cc_final: 0.6930 (m) REVERT: D 168 TRP cc_start: -0.2170 (t-100) cc_final: -0.2653 (t-100) REVERT: D 189 GLU cc_start: 0.5105 (pt0) cc_final: 0.4739 (mm-30) REVERT: D 190 MET cc_start: -0.0703 (tmm) cc_final: -0.0998 (ttp) REVERT: D 213 ASP cc_start: 0.1485 (t0) cc_final: 0.0924 (m-30) REVERT: D 221 GLN cc_start: 0.0324 (OUTLIER) cc_final: -0.0469 (mm-40) REVERT: D 294 THR cc_start: 0.2115 (p) cc_final: 0.1893 (t) REVERT: D 383 MET cc_start: 0.4155 (ptp) cc_final: 0.2588 (ppp) REVERT: D 474 MET cc_start: 0.1817 (mpp) cc_final: 0.1539 (mmm) REVERT: D 480 MET cc_start: -0.0602 (ptt) cc_final: -0.0820 (mtt) REVERT: D 559 ARG cc_start: 0.2395 (ptt90) cc_final: 0.1843 (tpt-90) REVERT: D 571 GLU cc_start: 0.2022 (OUTLIER) cc_final: 0.1716 (pt0) REVERT: F 323 MET cc_start: -0.1811 (tpt) cc_final: -0.2603 (ppp) REVERT: F 351 LEU cc_start: 0.1273 (OUTLIER) cc_final: 0.0820 (mp) REVERT: F 459 TRP cc_start: 0.0197 (t60) cc_final: -0.0301 (t60) REVERT: F 474 MET cc_start: -0.1592 (mmp) cc_final: -0.3173 (ttm) REVERT: F 502 SER cc_start: 0.2848 (OUTLIER) cc_final: 0.2630 (p) REVERT: H 166 GLU cc_start: 0.3895 (tp30) cc_final: 0.3124 (tt0) REVERT: H 383 MET cc_start: 0.0090 (mtp) cc_final: -0.0444 (tmm) REVERT: H 587 TYR cc_start: 0.2269 (OUTLIER) cc_final: 0.2016 (m-80) outliers start: 94 outliers final: 69 residues processed: 324 average time/residue: 0.2118 time to fit residues: 119.2535 Evaluate side-chains 312 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 234 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 317 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 119 optimal weight: 0.4980 chunk 301 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 299 optimal weight: 6.9990 chunk 294 optimal weight: 1.9990 chunk 379 optimal weight: 50.0000 chunk 313 optimal weight: 50.0000 chunk 157 optimal weight: 6.9990 chunk 468 optimal weight: 20.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 115 GLN A 207 HIS B 207 HIS C 907 ASN C 913 GLN C 935 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.251472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.199947 restraints weight = 60511.931| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 4.10 r_work: 0.3426 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.6944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 40695 Z= 0.267 Angle : 0.763 13.548 55522 Z= 0.369 Chirality : 0.049 0.445 6353 Planarity : 0.005 0.068 6984 Dihedral : 4.789 54.025 5140 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.61 % Favored : 93.11 % Rotamer: Outliers : 2.52 % Allowed : 16.47 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.12), residues: 4720 helix: 0.46 (0.13), residues: 1727 sheet: -1.03 (0.19), residues: 727 loop : -2.00 (0.12), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 983 TYR 0.024 0.002 TYR C1067 PHE 0.044 0.002 PHE A 86 TRP 0.015 0.001 TRP B1102 HIS 0.011 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.27 (40543) covalent geometry : angle 0.73398 / 0.36 (55114) SS BOND : bond 0.00412 / 0.27 ( 48) SS BOND : angle 2.17674 / 1.41 ( 96) hydrogen bonds : bond 0.05150 / 3.36 ( 1535) hydrogen bonds : angle 5.04665 / 3.42 ( 4386) link_BETA1-4 : bond 0.00582 / 0.34 ( 38) link_BETA1-4 : angle 2.03396 / 1.48 ( 114) link_NAG-ASN : bond 0.00534 / 0.31 ( 66) link_NAG-ASN : angle 2.90697 / 1.80 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 243 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7420 (mt) REVERT: A 379 CYS cc_start: 0.2594 (OUTLIER) cc_final: 0.1777 (p) REVERT: A 574 ASP cc_start: 0.7559 (p0) cc_final: 0.7331 (p0) REVERT: A 767 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8209 (mm) REVERT: A 1010 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.6107 (tp40) REVERT: B 153 MET cc_start: 0.0192 (ptm) cc_final: -0.0090 (ttp) REVERT: B 900 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8168 (mtp) REVERT: B 926 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: B 949 GLN cc_start: 0.8820 (tp40) cc_final: 0.8053 (mt0) REVERT: C 895 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8176 (pm20) REVERT: C 913 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: C 917 TYR cc_start: 0.8795 (m-80) cc_final: 0.8563 (m-80) REVERT: D 213 ASP cc_start: 0.1432 (t0) cc_final: 0.0984 (m-30) REVERT: D 221 GLN cc_start: 0.0221 (OUTLIER) cc_final: -0.0541 (mm-40) REVERT: D 383 MET cc_start: 0.4183 (ptp) cc_final: 0.2432 (ppp) REVERT: D 474 MET cc_start: 0.1790 (mpp) cc_final: 0.1567 (mmm) REVERT: D 480 MET cc_start: -0.0670 (ptt) cc_final: -0.0975 (mtt) REVERT: D 571 GLU cc_start: 0.2410 (OUTLIER) cc_final: 0.2043 (pt0) REVERT: F 152 MET cc_start: 0.0927 (ptt) cc_final: 0.0559 (ttp) REVERT: F 323 MET cc_start: -0.2099 (tpt) cc_final: -0.2876 (ppp) REVERT: F 351 LEU cc_start: 0.1330 (OUTLIER) cc_final: 0.0891 (mp) REVERT: F 376 MET cc_start: 0.1451 (mmm) cc_final: 0.1243 (mmt) REVERT: F 459 TRP cc_start: -0.0011 (t60) cc_final: -0.0449 (t60) REVERT: F 474 MET cc_start: -0.1551 (mmp) cc_final: -0.2934 (ttt) REVERT: F 587 TYR cc_start: -0.1105 (OUTLIER) cc_final: -0.1792 (m-10) REVERT: H 166 GLU cc_start: 0.4016 (tp30) cc_final: 0.3213 (tt0) REVERT: H 383 MET cc_start: 0.0378 (mtp) cc_final: -0.0227 (tmm) REVERT: H 587 TYR cc_start: 0.2408 (OUTLIER) cc_final: 0.2117 (m-80) outliers start: 106 outliers final: 76 residues processed: 334 average time/residue: 0.2092 time to fit residues: 121.7958 Evaluate side-chains 321 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 232 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 587 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 50 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 322 optimal weight: 50.0000 chunk 427 optimal weight: 1.9990 chunk 399 optimal weight: 20.0000 chunk 372 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 266 optimal weight: 0.6980 chunk 318 optimal weight: 20.0000 chunk 293 optimal weight: 0.4980 chunk 286 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN B 207 HIS B 239 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.256391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.205274 restraints weight = 59181.299| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 3.99 r_work: 0.3525 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.6994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40695 Z= 0.115 Angle : 0.641 11.413 55522 Z= 0.306 Chirality : 0.045 0.378 6353 Planarity : 0.004 0.061 6984 Dihedral : 4.431 53.297 5138 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.89 % Favored : 94.83 % Rotamer: Outliers : 1.66 % Allowed : 17.37 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4720 helix: 0.81 (0.13), residues: 1734 sheet: -0.81 (0.19), residues: 689 loop : -1.83 (0.12), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG B 983 TYR 0.023 0.001 TYR A1067 PHE 0.042 0.001 PHE A 86 TRP 0.036 0.001 TRP D 478 HIS 0.008 0.001 HIS H 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (40543) covalent geometry : angle 0.61720 / 0.30 (55114) SS BOND : bond 0.00289 / 0.19 ( 48) SS BOND : angle 1.58511 / 1.06 ( 96) hydrogen bonds : bond 0.03805 / 2.45 ( 1535) hydrogen bonds : angle 4.71845 / 3.20 ( 4386) link_BETA1-4 : bond 0.00549 / 0.30 ( 38) link_BETA1-4 : angle 1.90565 / 1.39 ( 114) link_NAG-ASN : bond 0.00403 / 0.24 ( 66) link_NAG-ASN : angle 2.40506 / 1.50 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 237 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 CYS cc_start: 0.2654 (OUTLIER) cc_final: 0.1822 (p) REVERT: A 767 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7979 (mm) REVERT: A 950 ASP cc_start: 0.8377 (m-30) cc_final: 0.8030 (m-30) REVERT: A 1010 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.5849 (tp40) REVERT: B 309 GLU cc_start: 0.7840 (tp30) cc_final: 0.7508 (tt0) REVERT: B 926 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: C 200 TYR cc_start: 0.7650 (m-80) cc_final: 0.7358 (m-80) REVERT: C 955 ASN cc_start: 0.7288 (m-40) cc_final: 0.6718 (t0) REVERT: D 189 GLU cc_start: 0.3038 (tp30) cc_final: 0.2464 (pt0) REVERT: D 221 GLN cc_start: 0.0291 (OUTLIER) cc_final: -0.0486 (mm-40) REVERT: D 287 GLN cc_start: 0.5353 (tp40) cc_final: 0.4140 (tm-30) REVERT: D 383 MET cc_start: 0.4111 (ptp) cc_final: 0.2405 (ppp) REVERT: D 474 MET cc_start: 0.1834 (mpp) cc_final: 0.1480 (mmm) REVERT: D 480 MET cc_start: -0.0805 (ptt) cc_final: -0.1239 (mtt) REVERT: D 571 GLU cc_start: 0.2389 (OUTLIER) cc_final: 0.2014 (pt0) REVERT: F 152 MET cc_start: 0.0932 (ptt) cc_final: 0.0568 (ttp) REVERT: F 323 MET cc_start: -0.2126 (tpt) cc_final: -0.2838 (ppp) REVERT: F 351 LEU cc_start: 0.1171 (OUTLIER) cc_final: 0.0752 (mp) REVERT: F 376 MET cc_start: 0.1347 (mmm) cc_final: 0.1095 (mmt) REVERT: F 459 TRP cc_start: -0.0030 (t60) cc_final: -0.0443 (t60) REVERT: F 474 MET cc_start: -0.1482 (mmp) cc_final: -0.3146 (ttm) REVERT: F 579 MET cc_start: -0.1907 (pmm) cc_final: -0.2207 (ttp) REVERT: F 587 TYR cc_start: -0.1021 (OUTLIER) cc_final: -0.1646 (m-10) REVERT: H 166 GLU cc_start: 0.3988 (tp30) cc_final: 0.3242 (tt0) REVERT: H 383 MET cc_start: 0.0522 (mtp) cc_final: -0.0056 (tmm) REVERT: H 408 MET cc_start: 0.2743 (mmt) cc_final: 0.2531 (mmt) REVERT: H 587 TYR cc_start: 0.2142 (OUTLIER) cc_final: 0.1918 (m-80) outliers start: 70 outliers final: 54 residues processed: 299 average time/residue: 0.2120 time to fit residues: 110.6014 Evaluate side-chains 291 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 228 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 587 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 587 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 304 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 387 optimal weight: 50.0000 chunk 119 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 421 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 302 optimal weight: 9.9990 chunk 188 optimal weight: 0.0980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN C 87 ASN ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.254306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.204678 restraints weight = 59092.644| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 3.85 r_work: 0.3499 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.7113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40695 Z= 0.164 Angle : 0.659 11.207 55522 Z= 0.316 Chirality : 0.046 0.397 6353 Planarity : 0.004 0.065 6984 Dihedral : 4.436 54.746 5138 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.83 % Favored : 93.90 % Rotamer: Outliers : 1.85 % Allowed : 17.21 % Favored : 80.94 % 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: -0.99 (0.12), residues: 4720 helix: 0.80 (0.13), residues: 1733 sheet: -0.74 (0.19), residues: 741 loop : -1.83 (0.12), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 983 TYR 0.021 0.001 TYR C1067 PHE 0.037 0.001 PHE A 86 TRP 0.030 0.001 TRP D 478 HIS 0.008 0.001 HIS H 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (40543) covalent geometry : angle 0.63397 / 0.31 (55114) SS BOND : bond 0.00342 / 0.23 ( 48) SS BOND : angle 1.77960 / 1.16 ( 96) hydrogen bonds : bond 0.04185 / 2.72 ( 1535) hydrogen bonds : angle 4.75435 / 3.23 ( 4386) link_BETA1-4 : bond 0.00550 / 0.31 ( 38) link_BETA1-4 : angle 1.90059 / 1.38 ( 114) link_NAG-ASN : bond 0.00390 / 0.23 ( 66) link_NAG-ASN : angle 2.47937 / 1.54 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11001.08 seconds wall clock time: 189 minutes 2.63 seconds (11342.63 seconds total)