Starting phenix.real_space_refine on Fri Mar 6 20:15:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y20_33577/03_2026/7y20_33577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y20_33577/03_2026/7y20_33577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y20_33577/03_2026/7y20_33577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y20_33577/03_2026/7y20_33577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y20_33577/03_2026/7y20_33577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y20_33577/03_2026/7y20_33577.map" } resolution = 3.8 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= 0.007 sd= 0.065 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 164 5.16 5 C 21851 2.51 5 N 5568 2.21 5 O 6686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34269 Number of models: 1 Model: "" Number of chains: 43 Chain: "A" 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: "B" Number of atoms: 7553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7553 Classifications: {'peptide': 963} Link IDs: {'PTRANS': 52, 'TRANS': 910} Chain breaks: 10 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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 dihedrals: 24 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.00, per 1000 atoms: 0.23 Number of scatterers: 34269 At special positions: 0 Unit cell: (134.788, 194.573, 250.01, 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 164 16.00 O 6686 8.00 N 5568 7.00 C 21851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, 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=1.97 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=1.85 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=1.84 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=1.80 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=2.08 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.20 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=1.83 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.39 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.12 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.18 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.07 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.14 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=1.86 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 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=2.26 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.97 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.17 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.10 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=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " NAG-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 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 B1409 " - " ASN B 709 " " 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 1 " - " ASN A 709 " " 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 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 331 " " NAG V 1 " - " ASN C 343 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " " NAG c 1 " - " ASN D 53 " " NAG d 1 " - " ASN D 90 " " NAG e 1 " - " ASN D 103 " " NAG f 1 " - " ASN D 432 " " NAG g 1 " - " ASN D 546 " " NAG h 1 " - " ASN F 53 " " NAG i 1 " - " ASN F 90 " " NAG j 1 " - " ASN F 103 " " NAG k 1 " - " ASN F 432 " " NAG l 1 " - " ASN F 546 " Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.2 seconds 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7818 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 47 sheets defined 36.4% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.679A 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 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 753 Processing helix chain 'A' and resid 754 through 756 No H-bonds generated for 'chain 'A' and resid 754 through 756' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 933 Processing helix chain 'A' and resid 933 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.322A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.810A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.491A pdb=" N ARG B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.529A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (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: 3.791A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.701A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.703A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.758A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.982A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.502A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.679A 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: 3.803A 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: 4.669A 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 747 through 754 removed outlier: 4.087A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.515A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.650A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.077A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 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: 4.155A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.286A 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: 3.909A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.215A 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: 3.935A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.931A 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: 3.566A 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: 3.731A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.259A 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: 3.905A 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: 4.083A 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: 4.296A 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: 4.179A 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: 3.729A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.652A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.692A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.980A 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: 3.563A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.578A 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: 4.608A 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: 3.537A 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: 4.097A 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: 3.594A 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: 3.832A 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: 4.216A 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: 3.934A pdb=" N LEU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 3.930A 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: 3.732A 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: 3.904A 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: 3.784A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.728A 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: 3.562A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 3.813A 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: 3.819A 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: 3.564A pdb=" N ILE F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.578A 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: 3.930A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 4.144A 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: 3.537A 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 sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.686A 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: 7.499A 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: 6.422A 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: 5.090A 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: 6.609A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.351A 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: 6.345A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.339A 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: 5.735A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (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 323 through 328 removed outlier: 3.953A pdb=" N ASN A 540 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER A 325 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ASN A 542 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 327 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.523A 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: 3.803A 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: 6.082A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (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 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.721A 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: 6.892A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.302A 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: 5.638A 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 1122 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: 3.507A 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: 7.498A 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: 6.422A 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: 6.924A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.629A 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: 5.162A 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: 5.058A 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: 3.602A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (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: 5.716A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) 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 358 removed outlier: 3.777A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.173A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.411A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.753A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.753A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.851A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, 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=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 6.904A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.078A 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=AD5, 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: 6.629A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.090A 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: 3.765A 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: 8.340A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.951A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 328 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.797A 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=AE1, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.812A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 553 through 554 removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.541A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.474A 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: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.740A 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: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.498A 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 1125 removed outlier: 4.944A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 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: 5.806A 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 1341 hydrogen bonds defined for protein. 3732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.59 Time building geometry restraints manager: 3.98 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: 7327 1.33 - 1.45: 9441 1.45 - 1.58: 18082 1.58 - 1.71: 0 1.71 - 1.83: 233 Bond restraints: 35083 Sorted by residual: bond pdb=" C TYR C 655 " pdb=" N VAL C 656 " ideal model delta sigma weight residual 1.329 1.434 -0.105 1.07e-02 8.73e+03 9.69e+01 bond pdb=" CA SER B 698 " pdb=" C SER B 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 2.33e+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 2.32e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.20e-02 6.94e+03 2.29e+01 ... (remaining 35078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 46818 2.70 - 5.40: 794 5.40 - 8.11: 59 8.11 - 10.81: 19 10.81 - 13.51: 7 Bond angle restraints: 47697 Sorted by residual: angle pdb=" N PHE D 28 " pdb=" CA PHE D 28 " pdb=" C PHE D 28 " ideal model delta sigma weight residual 111.24 101.83 9.41 1.29e+00 6.01e-01 5.32e+01 angle pdb=" N PHE F 28 " pdb=" CA PHE F 28 " pdb=" C PHE F 28 " ideal model delta sigma weight residual 111.24 101.87 9.37 1.29e+00 6.01e-01 5.28e+01 angle pdb=" N SER A 591 " pdb=" CA SER A 591 " pdb=" C SER A 591 " ideal model delta sigma weight residual 110.24 120.40 -10.16 1.47e+00 4.63e-01 4.78e+01 angle pdb=" N LEU D 45 " pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 111.07 103.93 7.14 1.07e+00 8.73e-01 4.45e+01 angle pdb=" N LEU F 45 " pdb=" CA LEU F 45 " pdb=" C LEU F 45 " ideal model delta sigma weight residual 111.07 103.96 7.11 1.07e+00 8.73e-01 4.41e+01 ... (remaining 47692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 20465 17.68 - 35.36: 1164 35.36 - 53.04: 313 53.04 - 70.72: 72 70.72 - 88.41: 56 Dihedral angle restraints: 22070 sinusoidal: 9940 harmonic: 12130 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.69 -69.31 1 1.00e+01 1.00e-02 6.21e+01 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 -18.16 -67.84 1 1.00e+01 1.00e-02 5.98e+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 -23.72 -62.28 1 1.00e+01 1.00e-02 5.13e+01 ... (remaining 22067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.334: 5540 0.334 - 0.669: 3 0.669 - 1.003: 2 1.003 - 1.338: 1 1.338 - 1.672: 3 Chirality restraints: 5549 Sorted by residual: 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 -1.28 -1.12 2.00e-02 2.50e+03 3.16e+03 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.73 -1.67 2.00e-01 2.50e+01 6.99e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.80e+01 ... (remaining 5546 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.193 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" CG ASN B 331 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.506 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " -0.348 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.197 2.00e-02 2.50e+03 2.43e-01 7.41e+02 pdb=" CG ASN B 343 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.415 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.129 2.00e-02 2.50e+03 2.04e-01 5.21e+02 pdb=" CG ASN A 331 " -0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.362 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.231 2.00e-02 2.50e+03 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 327 2.61 - 3.18: 29767 3.18 - 3.75: 48149 3.75 - 4.33: 69884 4.33 - 4.90: 113197 Nonbonded interactions: 261324 Sorted by model distance: nonbonded pdb=" O VAL A 445 " pdb=" OG SER A 446 " model vdw 2.034 3.040 nonbonded pdb=" O VAL C 445 " pdb=" OG SER C 446 " model vdw 2.034 3.040 nonbonded pdb=" O PRO C 39 " pdb=" CG ASP C 40 " model vdw 2.114 3.270 nonbonded pdb=" O CYS B 590 " pdb=" O SER B 591 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR C 333 " pdb=" N ASN C 334 " model vdw 2.207 3.120 ... (remaining 261319 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 454 or resid 491 through 1408)) selection = (chain 'B' and (resid 27 through 939 or resid 944 through 1408)) selection = (chain 'C' and (resid 27 through 454 or resid 491 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.620 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 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 : 0.009 0.356 35220 Z= 0.490 Angle : 1.088 48.934 48064 Z= 0.593 Chirality : 0.073 1.672 5549 Planarity : 0.005 0.104 6036 Dihedral : 12.640 88.406 14120 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 1.66 % Allowed : 6.53 % Favored : 91.80 % Rotamer: Outliers : 1.31 % Allowed : 3.99 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.11), residues: 4087 helix: -1.56 (0.12), residues: 1308 sheet: -0.92 (0.19), residues: 655 loop : -2.67 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.026 0.001 TYR B 453 PHE 0.038 0.001 PHE B 377 TRP 0.013 0.001 TRP D 594 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00773 (35083) covalent geometry : angle 0.90992 (47697) SS BOND : bond 0.10582 ( 44) SS BOND : angle 7.06087 ( 88) hydrogen bonds : bond 0.20754 ( 1312) hydrogen bonds : angle 8.06157 ( 3732) link_BETA1-4 : bond 0.01482 ( 33) link_BETA1-4 : angle 6.13880 ( 99) link_NAG-ASN : bond 0.02674 ( 60) link_NAG-ASN : angle 7.18895 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 636 time to evaluate : 0.823 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: A 221 SER cc_start: 0.5581 (t) cc_final: 0.5335 (p) REVERT: A 525 CYS cc_start: 0.4024 (OUTLIER) cc_final: 0.3735 (m) REVERT: B 390 LEU cc_start: 0.7942 (tp) cc_final: 0.7707 (tp) REVERT: B 1037 SER cc_start: 0.8677 (t) cc_final: 0.8462 (t) REVERT: C 270 LEU cc_start: 0.6450 (mt) cc_final: 0.5954 (mp) REVERT: D 37 GLU cc_start: 0.0176 (OUTLIER) cc_final: -0.0304 (tt0) REVERT: D 322 ASN cc_start: 0.2241 (m-40) cc_final: 0.1785 (m110) REVERT: D 323 MET cc_start: 0.2118 (mmp) cc_final: 0.1748 (mmp) REVERT: D 474 MET cc_start: -0.0046 (mmp) cc_final: -0.1829 (mmt) REVERT: F 28 PHE cc_start: 0.0549 (t80) cc_final: -0.0288 (t80) REVERT: F 37 GLU cc_start: -0.0595 (OUTLIER) cc_final: -0.1816 (mt-10) REVERT: F 327 PHE cc_start: 0.5146 (t80) cc_final: 0.4731 (t80) REVERT: F 510 TYR cc_start: 0.3405 (m-80) cc_final: 0.2821 (t80) outliers start: 48 outliers final: 13 residues processed: 680 average time/residue: 0.2061 time to fit residues: 228.1564 Evaluate side-chains 273 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 257 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 531 THR 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 587 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 351 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.0020 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 overall best weight: 2.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 417 ASN A 641 ASN A 992 GLN A1005 GLN B 207 HIS B 314 GLN B 856 ASN B1088 HIS C 207 HIS C 417 ASN C 556 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C1005 GLN D 101 GLN D 137 ASN D 277 ASN D 394 ASN D 417 HIS D 442 GLN D 472 GLN D 580 ASN D 599 ASN F 24 GLN F 101 GLN F 137 ASN F 277 ASN F 373 HIS F 417 HIS F 472 GLN F 599 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.195709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.123677 restraints weight = 89605.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.111109 restraints weight = 76977.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109272 restraints weight = 71132.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.108599 restraints weight = 54044.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108241 restraints weight = 43473.165| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 35220 Z= 0.180 Angle : 0.773 12.252 48064 Z= 0.378 Chirality : 0.049 0.570 5549 Planarity : 0.005 0.071 6036 Dihedral : 6.866 71.646 6445 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.53 % Favored : 94.10 % Rotamer: Outliers : 2.57 % Allowed : 10.51 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.12), residues: 4087 helix: -0.15 (0.14), residues: 1343 sheet: -0.89 (0.19), residues: 619 loop : -2.27 (0.12), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1019 TYR 0.025 0.001 TYR A1138 PHE 0.034 0.002 PHE F 512 TRP 0.024 0.001 TRP B 64 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00397 (35083) covalent geometry : angle 0.73389 (47697) SS BOND : bond 0.00635 ( 44) SS BOND : angle 2.33630 ( 88) hydrogen bonds : bond 0.05374 ( 1312) hydrogen bonds : angle 5.74531 ( 3732) link_BETA1-4 : bond 0.00701 ( 33) link_BETA1-4 : angle 2.46959 ( 99) link_NAG-ASN : bond 0.00873 ( 60) link_NAG-ASN : angle 3.27961 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 276 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8211 (pmm) cc_final: 0.7662 (pmm) REVERT: B 122 ASN cc_start: 0.2709 (OUTLIER) cc_final: 0.2402 (p0) REVERT: B 270 LEU cc_start: 0.7647 (mp) cc_final: 0.7402 (mp) REVERT: B 315 THR cc_start: 0.8650 (p) cc_final: 0.8423 (p) REVERT: B 357 ARG cc_start: 0.6059 (mtp85) cc_final: 0.5823 (mmm-85) REVERT: B 390 LEU cc_start: 0.8572 (tp) cc_final: 0.8335 (mp) REVERT: B 752 LEU cc_start: 0.9134 (tp) cc_final: 0.8900 (tp) REVERT: B 869 MET cc_start: 0.8493 (mmt) cc_final: 0.8063 (mpp) REVERT: B 1005 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7837 (tm-30) REVERT: C 153 MET cc_start: 0.5893 (tmm) cc_final: 0.5660 (tmm) REVERT: C 270 LEU cc_start: 0.7716 (mt) cc_final: 0.7280 (mp) REVERT: C 950 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7613 (t0) REVERT: C 977 LEU cc_start: 0.7578 (mp) cc_final: 0.7242 (mp) REVERT: C 979 ASP cc_start: 0.8648 (m-30) cc_final: 0.7973 (p0) REVERT: D 249 MET cc_start: -0.0246 (mtt) cc_final: -0.0600 (ptt) REVERT: D 323 MET cc_start: 0.1195 (mmp) cc_final: 0.0727 (mmp) REVERT: D 332 MET cc_start: -0.0677 (mmm) cc_final: -0.1175 (tpp) REVERT: D 376 MET cc_start: 0.3544 (ptt) cc_final: 0.1674 (tpp) REVERT: D 455 MET cc_start: 0.3226 (tmm) cc_final: 0.2761 (ttp) REVERT: D 474 MET cc_start: -0.1113 (mmp) cc_final: -0.2170 (tmm) REVERT: F 28 PHE cc_start: 0.0641 (t80) cc_final: -0.0042 (t80) REVERT: F 123 MET cc_start: 0.0647 (ttp) cc_final: 0.0327 (ptt) REVERT: F 327 PHE cc_start: 0.1251 (t80) cc_final: 0.0585 (t80) REVERT: F 383 MET cc_start: 0.0376 (mtp) cc_final: -0.0558 (tmm) outliers start: 94 outliers final: 38 residues processed: 353 average time/residue: 0.1971 time to fit residues: 116.3265 Evaluate side-chains 242 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 363 optimal weight: 8.9990 chunk 217 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 253 optimal weight: 0.0070 chunk 164 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 234 optimal weight: 50.0000 chunk 202 optimal weight: 7.9990 chunk 310 optimal weight: 40.0000 chunk 319 optimal weight: 40.0000 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 675 GLN A1002 GLN A1005 GLN C 207 HIS C 450 ASN C 556 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 GLN F 524 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.195370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.127057 restraints weight = 89126.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.115664 restraints weight = 74407.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.112404 restraints weight = 82678.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109577 restraints weight = 58768.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.110041 restraints weight = 42998.925| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35220 Z= 0.140 Angle : 0.686 21.316 48064 Z= 0.330 Chirality : 0.046 0.677 5549 Planarity : 0.004 0.049 6036 Dihedral : 6.128 59.612 6408 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.06 % Favored : 94.62 % Rotamer: Outliers : 2.24 % Allowed : 11.41 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 4087 helix: 0.45 (0.14), residues: 1332 sheet: -0.59 (0.19), residues: 641 loop : -1.98 (0.12), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1019 TYR 0.017 0.001 TYR A1138 PHE 0.032 0.002 PHE D 315 TRP 0.021 0.001 TRP A 104 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00300 (35083) covalent geometry : angle 0.65017 (47697) SS BOND : bond 0.00303 ( 44) SS BOND : angle 1.71408 ( 88) hydrogen bonds : bond 0.04510 ( 1312) hydrogen bonds : angle 5.31894 ( 3732) link_BETA1-4 : bond 0.00596 ( 33) link_BETA1-4 : angle 2.14443 ( 99) link_NAG-ASN : bond 0.00653 ( 60) link_NAG-ASN : angle 3.12474 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 231 time to evaluate : 1.244 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 153 MET cc_start: 0.4300 (ppp) cc_final: 0.4066 (ppp) REVERT: A 194 PHE cc_start: 0.7284 (m-10) cc_final: 0.7038 (m-10) REVERT: A 697 MET cc_start: 0.8386 (pmm) cc_final: 0.7677 (pmm) REVERT: A 988 GLU cc_start: 0.8565 (tp30) cc_final: 0.8122 (tm-30) REVERT: B 122 ASN cc_start: 0.2701 (OUTLIER) cc_final: 0.2456 (p0) REVERT: B 315 THR cc_start: 0.8529 (p) cc_final: 0.8311 (p) REVERT: B 390 LEU cc_start: 0.8984 (tp) cc_final: 0.8713 (mp) REVERT: B 752 LEU cc_start: 0.9240 (tp) cc_final: 0.9000 (tp) REVERT: B 869 MET cc_start: 0.8584 (mmt) cc_final: 0.7984 (mpp) REVERT: B 1005 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 88 ASP cc_start: 0.7111 (p0) cc_final: 0.6866 (p0) REVERT: C 270 LEU cc_start: 0.7846 (mt) cc_final: 0.7399 (mp) REVERT: C 336 CYS cc_start: 0.6479 (OUTLIER) cc_final: 0.5847 (p) REVERT: C 822 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9258 (mm) REVERT: C 977 LEU cc_start: 0.7492 (mp) cc_final: 0.7220 (mp) REVERT: C 979 ASP cc_start: 0.8682 (m-30) cc_final: 0.8145 (p0) REVERT: D 82 MET cc_start: 0.1763 (OUTLIER) cc_final: 0.1537 (tmm) REVERT: D 190 MET cc_start: 0.4387 (tmm) cc_final: 0.4026 (ptm) REVERT: D 332 MET cc_start: -0.1129 (mmm) cc_final: -0.1453 (ttm) REVERT: D 455 MET cc_start: 0.3114 (tmm) cc_final: 0.2458 (ttp) REVERT: D 474 MET cc_start: -0.1239 (mmp) cc_final: -0.2060 (tmm) REVERT: F 123 MET cc_start: 0.0260 (ttp) cc_final: -0.0163 (ptt) REVERT: F 152 MET cc_start: -0.3973 (mtt) cc_final: -0.4421 (mmt) REVERT: F 249 MET cc_start: 0.1780 (ptp) cc_final: 0.0949 (tpp) REVERT: F 383 MET cc_start: -0.0048 (mtp) cc_final: -0.0931 (tmm) outliers start: 82 outliers final: 40 residues processed: 302 average time/residue: 0.1879 time to fit residues: 97.1398 Evaluate side-chains 235 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 255 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 410 optimal weight: 10.0000 chunk 13 optimal weight: 0.0370 chunk 243 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B1071 GLN C 207 HIS C 271 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 373 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.191259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.115198 restraints weight = 86836.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.104011 restraints weight = 70478.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101995 restraints weight = 76711.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101705 restraints weight = 54918.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101610 restraints weight = 44188.965| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 35220 Z= 0.202 Angle : 0.721 14.405 48064 Z= 0.349 Chirality : 0.049 0.886 5549 Planarity : 0.004 0.045 6036 Dihedral : 5.815 58.465 6408 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.51 % Favored : 94.20 % Rotamer: Outliers : 2.52 % Allowed : 12.18 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 4087 helix: 0.56 (0.14), residues: 1361 sheet: -0.80 (0.20), residues: 582 loop : -1.91 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1019 TYR 0.022 0.002 TYR A 873 PHE 0.027 0.002 PHE D 315 TRP 0.036 0.001 TRP A 104 HIS 0.012 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00454 (35083) covalent geometry : angle 0.68806 (47697) SS BOND : bond 0.00516 ( 44) SS BOND : angle 2.06725 ( 88) hydrogen bonds : bond 0.04645 ( 1312) hydrogen bonds : angle 5.20428 ( 3732) link_BETA1-4 : bond 0.00569 ( 33) link_BETA1-4 : angle 2.02108 ( 99) link_NAG-ASN : bond 0.00611 ( 60) link_NAG-ASN : angle 2.99274 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 223 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8269 (tp) cc_final: 0.7943 (mt) REVERT: A 153 MET cc_start: 0.4386 (OUTLIER) cc_final: 0.4135 (ppp) REVERT: A 270 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8113 (mp) REVERT: A 317 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8639 (m-40) REVERT: A 697 MET cc_start: 0.8519 (pmm) cc_final: 0.8188 (ptp) REVERT: A 990 GLU cc_start: 0.7862 (pm20) cc_final: 0.7624 (pp20) REVERT: A 994 ASP cc_start: 0.8638 (m-30) cc_final: 0.8388 (m-30) REVERT: A 1001 LEU cc_start: 0.9443 (tp) cc_final: 0.9089 (tt) REVERT: B 984 LEU cc_start: 0.7981 (tp) cc_final: 0.7673 (tp) REVERT: B 1005 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 1050 MET cc_start: 0.7940 (ptp) cc_final: 0.7701 (ptp) REVERT: C 153 MET cc_start: 0.6065 (tmm) cc_final: 0.5853 (tmm) REVERT: C 336 CYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6738 (p) REVERT: C 756 TYR cc_start: 0.8470 (m-80) cc_final: 0.8228 (m-80) REVERT: C 822 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9291 (mm) REVERT: C 979 ASP cc_start: 0.8831 (m-30) cc_final: 0.8591 (m-30) REVERT: D 82 MET cc_start: 0.1641 (OUTLIER) cc_final: 0.1412 (tmm) REVERT: D 332 MET cc_start: -0.1216 (mmm) cc_final: -0.1537 (ttm) REVERT: D 376 MET cc_start: 0.2582 (ppp) cc_final: 0.0927 (ppp) REVERT: D 455 MET cc_start: 0.3457 (tmm) cc_final: 0.3152 (ttp) REVERT: D 474 MET cc_start: -0.1425 (mmp) cc_final: -0.1929 (tmm) REVERT: F 123 MET cc_start: 0.0489 (ttp) cc_final: -0.0417 (ptt) REVERT: F 152 MET cc_start: -0.4225 (mtt) cc_final: -0.4557 (mmt) REVERT: F 249 MET cc_start: 0.1830 (ptp) cc_final: 0.1113 (tpp) REVERT: F 297 MET cc_start: 0.0181 (mpp) cc_final: -0.1771 (tmm) REVERT: F 383 MET cc_start: -0.0209 (mtp) cc_final: -0.1214 (tmm) REVERT: F 512 PHE cc_start: 0.1771 (t80) cc_final: 0.1273 (t80) outliers start: 92 outliers final: 47 residues processed: 303 average time/residue: 0.1806 time to fit residues: 95.5045 Evaluate side-chains 242 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 115 optimal weight: 6.9990 chunk 390 optimal weight: 30.0000 chunk 6 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 114 optimal weight: 30.0000 chunk 28 optimal weight: 0.9980 chunk 369 optimal weight: 50.0000 chunk 336 optimal weight: 40.0000 chunk 315 optimal weight: 20.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 755 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B1135 ASN C 207 HIS C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN D 305 GLN D 374 HIS F 51 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.185911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.114642 restraints weight = 86940.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101000 restraints weight = 74821.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.098400 restraints weight = 72903.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097647 restraints weight = 52661.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097647 restraints weight = 48882.561| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 35220 Z= 0.320 Angle : 0.840 14.703 48064 Z= 0.410 Chirality : 0.050 0.568 5549 Planarity : 0.005 0.046 6036 Dihedral : 6.626 58.737 6406 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.44 % Favored : 93.27 % Rotamer: Outliers : 3.34 % Allowed : 12.91 % Favored : 83.75 % 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: -1.58 (0.12), residues: 4087 helix: 0.33 (0.14), residues: 1369 sheet: -1.10 (0.19), residues: 574 loop : -2.02 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 393 TYR 0.025 0.002 TYR A1067 PHE 0.031 0.003 PHE A 194 TRP 0.051 0.002 TRP A 104 HIS 0.016 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00729 (35083) covalent geometry : angle 0.80840 (47697) SS BOND : bond 0.00520 ( 44) SS BOND : angle 2.34721 ( 88) hydrogen bonds : bond 0.05203 ( 1312) hydrogen bonds : angle 5.46504 ( 3732) link_BETA1-4 : bond 0.00564 ( 33) link_BETA1-4 : angle 2.05689 ( 99) link_NAG-ASN : bond 0.00716 ( 60) link_NAG-ASN : angle 3.22195 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 194 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8270 (tp) cc_final: 0.7738 (mp) REVERT: A 238 PHE cc_start: 0.7154 (p90) cc_final: 0.6393 (p90) REVERT: A 270 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8200 (mp) REVERT: A 317 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8680 (m-40) REVERT: A 740 MET cc_start: 0.9246 (mmm) cc_final: 0.9033 (mmm) REVERT: A 960 ASN cc_start: 0.9004 (m-40) cc_final: 0.8659 (t0) REVERT: B 592 PHE cc_start: 0.7940 (p90) cc_final: 0.7728 (p90) REVERT: B 1005 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 1050 MET cc_start: 0.8358 (ptp) cc_final: 0.8026 (ptp) REVERT: C 336 CYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7046 (p) REVERT: C 537 LYS cc_start: 0.8794 (tttp) cc_final: 0.8069 (tttp) REVERT: C 867 ASP cc_start: 0.7946 (p0) cc_final: 0.7682 (p0) REVERT: C 959 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9358 (tt) REVERT: C 984 LEU cc_start: 0.8474 (tp) cc_final: 0.8208 (tp) REVERT: C 988 GLU cc_start: 0.8613 (mp0) cc_final: 0.8270 (tp30) REVERT: D 82 MET cc_start: 0.1335 (OUTLIER) cc_final: 0.0953 (tmm) REVERT: D 203 TRP cc_start: 0.0736 (OUTLIER) cc_final: 0.0511 (m-10) REVERT: D 332 MET cc_start: -0.1318 (mmm) cc_final: -0.1686 (ttm) REVERT: D 455 MET cc_start: 0.3866 (tmm) cc_final: 0.3463 (ttm) REVERT: D 474 MET cc_start: -0.1393 (mmp) cc_final: -0.1736 (tmm) REVERT: F 72 PHE cc_start: 0.1932 (t80) cc_final: 0.1698 (t80) REVERT: F 123 MET cc_start: -0.0302 (ttp) cc_final: -0.0714 (ptt) REVERT: F 249 MET cc_start: 0.1920 (ptp) cc_final: 0.1077 (tpp) REVERT: F 363 LYS cc_start: -0.1624 (mmtt) cc_final: -0.1923 (tppt) REVERT: F 383 MET cc_start: -0.0358 (mtp) cc_final: -0.1186 (tmm) REVERT: F 455 MET cc_start: 0.4122 (mmm) cc_final: 0.3665 (mmm) outliers start: 122 outliers final: 81 residues processed: 296 average time/residue: 0.1849 time to fit residues: 95.8434 Evaluate side-chains 249 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 162 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1023 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 MET Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 134 optimal weight: 0.0980 chunk 411 optimal weight: 50.0000 chunk 228 optimal weight: 20.0000 chunk 218 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 405 optimal weight: 0.1980 chunk 392 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 99 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 207 HIS C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN D 508 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.190863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.124720 restraints weight = 89316.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109657 restraints weight = 77880.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107290 restraints weight = 79303.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.107648 restraints weight = 55506.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.107076 restraints weight = 43381.982| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35220 Z= 0.118 Angle : 0.647 13.210 48064 Z= 0.313 Chirality : 0.046 0.591 5549 Planarity : 0.004 0.049 6036 Dihedral : 5.881 59.842 6406 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.45 % Favored : 95.30 % Rotamer: Outliers : 1.92 % Allowed : 14.12 % Favored : 83.97 % 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: -1.05 (0.13), residues: 4087 helix: 0.93 (0.15), residues: 1338 sheet: -0.64 (0.19), residues: 633 loop : -1.85 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.019 0.001 TYR A 91 PHE 0.021 0.001 PHE C 86 TRP 0.037 0.001 TRP A 104 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00250 (35083) covalent geometry : angle 0.61868 (47697) SS BOND : bond 0.00442 ( 44) SS BOND : angle 1.80198 ( 88) hydrogen bonds : bond 0.04198 ( 1312) hydrogen bonds : angle 4.93758 ( 3732) link_BETA1-4 : bond 0.00592 ( 33) link_BETA1-4 : angle 1.89596 ( 99) link_NAG-ASN : bond 0.00456 ( 60) link_NAG-ASN : angle 2.58529 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 204 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8244 (tp) cc_final: 0.7776 (mt) REVERT: A 153 MET cc_start: 0.4884 (pmm) cc_final: 0.4392 (ppp) REVERT: A 189 LEU cc_start: 0.8514 (mt) cc_final: 0.8215 (tp) REVERT: A 238 PHE cc_start: 0.7396 (p90) cc_final: 0.6612 (p90) REVERT: A 968 SER cc_start: 0.9204 (m) cc_final: 0.8714 (p) REVERT: A 988 GLU cc_start: 0.8542 (tp30) cc_final: 0.8334 (tm-30) REVERT: A 1001 LEU cc_start: 0.9352 (tp) cc_final: 0.9093 (tt) REVERT: B 869 MET cc_start: 0.8656 (mmt) cc_final: 0.8228 (mpp) REVERT: B 1050 MET cc_start: 0.7835 (ptp) cc_final: 0.7511 (ptp) REVERT: C 55 PHE cc_start: 0.8416 (m-80) cc_final: 0.8101 (m-80) REVERT: C 153 MET cc_start: 0.5667 (ttp) cc_final: 0.5207 (tmm) REVERT: C 336 CYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6915 (p) REVERT: C 959 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9334 (tt) REVERT: C 969 LYS cc_start: 0.9452 (mmtt) cc_final: 0.9159 (mmtp) REVERT: C 984 LEU cc_start: 0.8494 (tp) cc_final: 0.8198 (tp) REVERT: C 988 GLU cc_start: 0.8494 (mp0) cc_final: 0.8268 (tp30) REVERT: D 82 MET cc_start: 0.1248 (OUTLIER) cc_final: 0.0862 (tmm) REVERT: D 190 MET cc_start: 0.4498 (tmm) cc_final: 0.4294 (ppp) REVERT: D 203 TRP cc_start: 0.0902 (OUTLIER) cc_final: 0.0677 (m-10) REVERT: D 332 MET cc_start: -0.1273 (mmm) cc_final: -0.1661 (ttm) REVERT: D 455 MET cc_start: 0.4003 (tmm) cc_final: 0.3623 (ttm) REVERT: D 474 MET cc_start: -0.1119 (mmp) cc_final: -0.1426 (tmm) REVERT: F 72 PHE cc_start: 0.1904 (t80) cc_final: 0.1612 (t80) REVERT: F 123 MET cc_start: -0.0402 (ttp) cc_final: -0.1132 (ptm) REVERT: F 249 MET cc_start: 0.1706 (ptp) cc_final: 0.0911 (tpp) REVERT: F 297 MET cc_start: -0.0350 (mpp) cc_final: -0.1878 (tmm) REVERT: F 360 MET cc_start: 0.0822 (mmm) cc_final: 0.0586 (mmm) REVERT: F 363 LYS cc_start: -0.1647 (mmtt) cc_final: -0.1983 (tppt) REVERT: F 383 MET cc_start: -0.0251 (mtp) cc_final: -0.0935 (tmm) REVERT: F 455 MET cc_start: 0.5320 (mmm) cc_final: 0.5049 (mmm) outliers start: 70 outliers final: 42 residues processed: 266 average time/residue: 0.1900 time to fit residues: 88.3070 Evaluate side-chains 221 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 MET Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 125 optimal weight: 3.9990 chunk 392 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 204 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 31 optimal weight: 30.0000 chunk 131 optimal weight: 5.9990 chunk 357 optimal weight: 9.9990 chunk 327 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN D 522 GLN F 556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.188203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.108360 restraints weight = 93313.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097111 restraints weight = 71658.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.095018 restraints weight = 65899.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095617 restraints weight = 50984.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.095031 restraints weight = 47191.707| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35220 Z= 0.198 Angle : 0.685 13.109 48064 Z= 0.332 Chirality : 0.046 0.558 5549 Planarity : 0.004 0.069 6036 Dihedral : 5.886 59.469 6406 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.77 % Favored : 93.98 % Rotamer: Outliers : 2.46 % Allowed : 14.17 % Favored : 83.37 % 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: -1.11 (0.13), residues: 4087 helix: 0.85 (0.14), residues: 1368 sheet: -0.79 (0.20), residues: 570 loop : -1.84 (0.12), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1019 TYR 0.027 0.001 TYR F 183 PHE 0.024 0.002 PHE D 315 TRP 0.046 0.001 TRP A 104 HIS 0.010 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00447 (35083) covalent geometry : angle 0.65623 (47697) SS BOND : bond 0.00390 ( 44) SS BOND : angle 1.95982 ( 88) hydrogen bonds : bond 0.04426 ( 1312) hydrogen bonds : angle 5.00184 ( 3732) link_BETA1-4 : bond 0.00532 ( 33) link_BETA1-4 : angle 1.88799 ( 99) link_NAG-ASN : bond 0.00513 ( 60) link_NAG-ASN : angle 2.67629 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 177 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8069 (tp) cc_final: 0.7650 (mt) REVERT: A 153 MET cc_start: 0.4865 (pmm) cc_final: 0.4446 (ppp) REVERT: A 189 LEU cc_start: 0.8545 (mt) cc_final: 0.8241 (tp) REVERT: A 238 PHE cc_start: 0.6733 (p90) cc_final: 0.6173 (p90) REVERT: A 740 MET cc_start: 0.9294 (tpp) cc_final: 0.8687 (tpp) REVERT: A 968 SER cc_start: 0.9393 (m) cc_final: 0.8874 (p) REVERT: A 1001 LEU cc_start: 0.9445 (tp) cc_final: 0.9162 (tt) REVERT: B 780 GLU cc_start: 0.8684 (tp30) cc_final: 0.8417 (tm-30) REVERT: B 1050 MET cc_start: 0.8151 (ptp) cc_final: 0.7858 (ptp) REVERT: C 55 PHE cc_start: 0.8555 (m-80) cc_final: 0.8115 (m-80) REVERT: C 153 MET cc_start: 0.6533 (ttp) cc_final: 0.6181 (tmm) REVERT: C 398 ASP cc_start: 0.0100 (OUTLIER) cc_final: -0.0814 (t70) REVERT: C 867 ASP cc_start: 0.7963 (p0) cc_final: 0.7732 (p0) REVERT: C 959 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9094 (tt) REVERT: C 969 LYS cc_start: 0.9496 (mmtt) cc_final: 0.9209 (mmtp) REVERT: C 988 GLU cc_start: 0.8853 (mp0) cc_final: 0.8434 (tp30) REVERT: D 82 MET cc_start: 0.1655 (OUTLIER) cc_final: 0.1399 (tmm) REVERT: D 332 MET cc_start: -0.1008 (mmm) cc_final: -0.1328 (ttm) REVERT: D 455 MET cc_start: 0.3909 (tmm) cc_final: 0.3611 (ttm) REVERT: D 474 MET cc_start: -0.1281 (mmp) cc_final: -0.1809 (tmm) REVERT: F 123 MET cc_start: 0.1184 (ttp) cc_final: -0.0043 (ptm) REVERT: F 249 MET cc_start: 0.1575 (ptp) cc_final: 0.0986 (tpp) REVERT: F 363 LYS cc_start: -0.1541 (mmtt) cc_final: -0.1797 (tppt) REVERT: F 383 MET cc_start: -0.0149 (mtp) cc_final: -0.0666 (tmm) outliers start: 90 outliers final: 61 residues processed: 255 average time/residue: 0.1838 time to fit residues: 81.9218 Evaluate side-chains 229 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 165 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 MET Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 11 optimal weight: 5.9990 chunk 390 optimal weight: 0.1980 chunk 284 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 17 optimal weight: 0.0970 chunk 237 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 352 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1005 GLN C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.190718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114317 restraints weight = 93351.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.103509 restraints weight = 77020.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.101442 restraints weight = 74262.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.101266 restraints weight = 50346.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.100834 restraints weight = 41507.263| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35220 Z= 0.114 Angle : 0.629 12.525 48064 Z= 0.304 Chirality : 0.045 0.541 5549 Planarity : 0.004 0.062 6036 Dihedral : 5.513 59.902 6406 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer: Outliers : 1.53 % Allowed : 15.13 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4087 helix: 1.10 (0.15), residues: 1358 sheet: -0.50 (0.19), residues: 636 loop : -1.73 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1019 TYR 0.028 0.001 TYR F 183 PHE 0.026 0.001 PHE D 315 TRP 0.043 0.001 TRP A 104 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00241 (35083) covalent geometry : angle 0.60389 (47697) SS BOND : bond 0.00397 ( 44) SS BOND : angle 1.76456 ( 88) hydrogen bonds : bond 0.03941 ( 1312) hydrogen bonds : angle 4.77582 ( 3732) link_BETA1-4 : bond 0.00542 ( 33) link_BETA1-4 : angle 1.83619 ( 99) link_NAG-ASN : bond 0.00413 ( 60) link_NAG-ASN : angle 2.40738 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8174 (tp) cc_final: 0.7730 (mt) REVERT: A 153 MET cc_start: 0.4712 (pmm) cc_final: 0.4148 (ppp) REVERT: A 189 LEU cc_start: 0.8510 (mt) cc_final: 0.8185 (tp) REVERT: A 238 PHE cc_start: 0.6976 (p90) cc_final: 0.6250 (p90) REVERT: A 740 MET cc_start: 0.9308 (tpp) cc_final: 0.8968 (mmm) REVERT: A 968 SER cc_start: 0.9333 (m) cc_final: 0.8806 (p) REVERT: A 984 LEU cc_start: 0.7376 (tp) cc_final: 0.5622 (tp) REVERT: A 988 GLU cc_start: 0.9024 (tp30) cc_final: 0.8753 (tm-30) REVERT: A 1001 LEU cc_start: 0.9401 (tp) cc_final: 0.9151 (tt) REVERT: B 517 LEU cc_start: 0.1481 (OUTLIER) cc_final: 0.1275 (mp) REVERT: B 740 MET cc_start: 0.8702 (mmm) cc_final: 0.8469 (mmm) REVERT: B 761 THR cc_start: 0.8968 (m) cc_final: 0.8691 (p) REVERT: B 780 GLU cc_start: 0.8643 (tp30) cc_final: 0.8399 (tm-30) REVERT: B 869 MET cc_start: 0.8739 (mmt) cc_final: 0.8224 (mpp) REVERT: B 984 LEU cc_start: 0.8252 (tp) cc_final: 0.7828 (tp) REVERT: B 1050 MET cc_start: 0.7420 (ptp) cc_final: 0.7161 (ptp) REVERT: C 153 MET cc_start: 0.6241 (ttp) cc_final: 0.5888 (tmm) REVERT: C 867 ASP cc_start: 0.7785 (p0) cc_final: 0.7571 (p0) REVERT: C 969 LYS cc_start: 0.9478 (mmtt) cc_final: 0.9170 (mmtt) REVERT: C 988 GLU cc_start: 0.8789 (mp0) cc_final: 0.8382 (tp30) REVERT: D 82 MET cc_start: 0.1722 (OUTLIER) cc_final: 0.1447 (tmm) REVERT: D 86 GLN cc_start: 0.3495 (mp-120) cc_final: 0.2886 (pt0) REVERT: D 187 LYS cc_start: -0.0987 (mmmt) cc_final: -0.1367 (pptt) REVERT: D 332 MET cc_start: -0.1361 (mmm) cc_final: -0.1669 (ttm) REVERT: D 360 MET cc_start: 0.0430 (mmt) cc_final: -0.0974 (mmt) REVERT: D 455 MET cc_start: 0.3610 (tmm) cc_final: 0.3363 (ttm) REVERT: D 474 MET cc_start: -0.1280 (mmp) cc_final: -0.1891 (tmm) REVERT: F 123 MET cc_start: 0.1462 (ttp) cc_final: -0.0747 (ptm) REVERT: F 249 MET cc_start: 0.1566 (ptp) cc_final: 0.0985 (tpp) REVERT: F 297 MET cc_start: -0.0112 (mpp) cc_final: -0.1137 (ttp) REVERT: F 363 LYS cc_start: -0.1459 (mmtt) cc_final: -0.1719 (tppt) REVERT: F 383 MET cc_start: -0.0064 (mtp) cc_final: -0.0574 (tmm) outliers start: 56 outliers final: 41 residues processed: 236 average time/residue: 0.1786 time to fit residues: 73.7036 Evaluate side-chains 220 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 MET Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 125 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 287 optimal weight: 6.9990 chunk 379 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 286 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.190115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.120775 restraints weight = 91532.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.105784 restraints weight = 90971.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.103023 restraints weight = 90827.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.101344 restraints weight = 60309.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.101644 restraints weight = 49543.818| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35220 Z= 0.143 Angle : 0.642 12.437 48064 Z= 0.309 Chirality : 0.045 0.535 5549 Planarity : 0.004 0.056 6036 Dihedral : 5.454 59.805 6406 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.19 % Favored : 94.57 % Rotamer: Outliers : 1.83 % Allowed : 15.05 % Favored : 83.12 % 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: -0.80 (0.13), residues: 4087 helix: 1.15 (0.15), residues: 1356 sheet: -0.50 (0.19), residues: 652 loop : -1.74 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1019 TYR 0.027 0.001 TYR F 183 PHE 0.027 0.001 PHE C 275 TRP 0.061 0.001 TRP A 104 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00319 (35083) covalent geometry : angle 0.61611 (47697) SS BOND : bond 0.00403 ( 44) SS BOND : angle 1.88167 ( 88) hydrogen bonds : bond 0.03979 ( 1312) hydrogen bonds : angle 4.76935 ( 3732) link_BETA1-4 : bond 0.00518 ( 33) link_BETA1-4 : angle 1.81521 ( 99) link_NAG-ASN : bond 0.00403 ( 60) link_NAG-ASN : angle 2.42001 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 179 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8237 (tp) cc_final: 0.7770 (mt) REVERT: A 153 MET cc_start: 0.4557 (pmm) cc_final: 0.3799 (ppp) REVERT: A 189 LEU cc_start: 0.8277 (mt) cc_final: 0.7980 (tp) REVERT: A 238 PHE cc_start: 0.7193 (p90) cc_final: 0.6356 (p90) REVERT: A 740 MET cc_start: 0.9136 (tpp) cc_final: 0.8863 (mmm) REVERT: A 968 SER cc_start: 0.9322 (m) cc_final: 0.8903 (p) REVERT: A 984 LEU cc_start: 0.7515 (tp) cc_final: 0.6055 (tp) REVERT: A 988 GLU cc_start: 0.8942 (tp30) cc_final: 0.8697 (tm-30) REVERT: A 1001 LEU cc_start: 0.9344 (tp) cc_final: 0.9112 (tt) REVERT: B 517 LEU cc_start: 0.1188 (OUTLIER) cc_final: 0.0960 (mp) REVERT: B 740 MET cc_start: 0.8562 (mmm) cc_final: 0.8353 (mmm) REVERT: B 761 THR cc_start: 0.9054 (m) cc_final: 0.8850 (p) REVERT: B 869 MET cc_start: 0.8531 (mmt) cc_final: 0.8194 (mpp) REVERT: B 1050 MET cc_start: 0.7958 (ptp) cc_final: 0.7724 (ptp) REVERT: C 153 MET cc_start: 0.6046 (ttp) cc_final: 0.5763 (tmm) REVERT: C 867 ASP cc_start: 0.7603 (p0) cc_final: 0.7339 (p0) REVERT: C 969 LYS cc_start: 0.9454 (mmtt) cc_final: 0.9197 (mmtp) REVERT: C 988 GLU cc_start: 0.8561 (mp0) cc_final: 0.8279 (tp30) REVERT: D 82 MET cc_start: 0.1644 (OUTLIER) cc_final: 0.1319 (tmm) REVERT: D 86 GLN cc_start: 0.3470 (mp-120) cc_final: 0.2815 (pt0) REVERT: D 332 MET cc_start: -0.1397 (mmm) cc_final: -0.1702 (ttm) REVERT: D 360 MET cc_start: 0.0532 (mmt) cc_final: -0.0908 (mmt) REVERT: D 455 MET cc_start: 0.3686 (tmm) cc_final: 0.3428 (ttm) REVERT: D 474 MET cc_start: -0.1359 (mmp) cc_final: -0.1851 (tmm) REVERT: F 123 MET cc_start: 0.0866 (ttp) cc_final: -0.1129 (ptm) REVERT: F 249 MET cc_start: 0.1505 (ptp) cc_final: 0.0920 (tpp) REVERT: F 297 MET cc_start: 0.0349 (mpp) cc_final: -0.0867 (ttt) REVERT: F 363 LYS cc_start: -0.1476 (mmtt) cc_final: -0.1744 (tppt) REVERT: F 383 MET cc_start: -0.0118 (mtp) cc_final: -0.0651 (tmm) outliers start: 67 outliers final: 54 residues processed: 240 average time/residue: 0.1830 time to fit residues: 77.2178 Evaluate side-chains 230 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 MET Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 252 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 232 optimal weight: 50.0000 chunk 181 optimal weight: 1.9990 chunk 210 optimal weight: 0.0170 chunk 335 optimal weight: 7.9990 chunk 313 optimal weight: 50.0000 overall best weight: 0.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN C 207 HIS C 564 GLN D 380 GLN F 556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.191193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.124969 restraints weight = 95079.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.109218 restraints weight = 83360.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107344 restraints weight = 73010.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.106403 restraints weight = 48506.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.106817 restraints weight = 40906.513| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35220 Z= 0.110 Angle : 0.620 12.215 48064 Z= 0.299 Chirality : 0.045 0.526 5549 Planarity : 0.004 0.056 6036 Dihedral : 5.214 59.878 6406 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.55 % Favored : 95.20 % Rotamer: Outliers : 1.78 % Allowed : 15.21 % Favored : 83.01 % 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: -0.67 (0.13), residues: 4087 helix: 1.23 (0.15), residues: 1344 sheet: -0.41 (0.19), residues: 655 loop : -1.64 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1019 TYR 0.027 0.001 TYR F 183 PHE 0.033 0.001 PHE D 315 TRP 0.046 0.001 TRP A 104 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00234 (35083) covalent geometry : angle 0.59735 (47697) SS BOND : bond 0.00299 ( 44) SS BOND : angle 1.50958 ( 88) hydrogen bonds : bond 0.03732 ( 1312) hydrogen bonds : angle 4.68247 ( 3732) link_BETA1-4 : bond 0.00539 ( 33) link_BETA1-4 : angle 1.79878 ( 99) link_NAG-ASN : bond 0.00385 ( 60) link_NAG-ASN : angle 2.30338 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 186 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8173 (tp) cc_final: 0.7664 (mt) REVERT: A 153 MET cc_start: 0.4494 (pmm) cc_final: 0.2656 (mmm) REVERT: A 189 LEU cc_start: 0.8417 (mt) cc_final: 0.8200 (tp) REVERT: A 191 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7818 (mt-10) REVERT: A 238 PHE cc_start: 0.7192 (p90) cc_final: 0.6365 (p90) REVERT: A 740 MET cc_start: 0.9145 (tpp) cc_final: 0.8857 (mmm) REVERT: A 968 SER cc_start: 0.9272 (m) cc_final: 0.8919 (p) REVERT: A 984 LEU cc_start: 0.7548 (tp) cc_final: 0.6078 (tp) REVERT: A 988 GLU cc_start: 0.8783 (tp30) cc_final: 0.8547 (tm-30) REVERT: A 1001 LEU cc_start: 0.9334 (tp) cc_final: 0.9089 (tt) REVERT: B 517 LEU cc_start: 0.1396 (OUTLIER) cc_final: 0.1134 (mp) REVERT: B 740 MET cc_start: 0.8585 (mmm) cc_final: 0.8368 (mmm) REVERT: B 869 MET cc_start: 0.8612 (mmt) cc_final: 0.8156 (mpp) REVERT: B 984 LEU cc_start: 0.8201 (tp) cc_final: 0.7798 (tp) REVERT: C 867 ASP cc_start: 0.7587 (p0) cc_final: 0.7322 (p0) REVERT: C 969 LYS cc_start: 0.9457 (mmtt) cc_final: 0.9172 (mmtp) REVERT: C 984 LEU cc_start: 0.8554 (tp) cc_final: 0.8274 (tt) REVERT: C 988 GLU cc_start: 0.8551 (mp0) cc_final: 0.8323 (tp30) REVERT: D 82 MET cc_start: 0.1540 (OUTLIER) cc_final: 0.1190 (tmm) REVERT: D 86 GLN cc_start: 0.3449 (mp-120) cc_final: 0.2754 (pt0) REVERT: D 270 MET cc_start: -0.4352 (mpp) cc_final: -0.4685 (mtm) REVERT: D 332 MET cc_start: -0.1059 (mmm) cc_final: -0.1364 (ttm) REVERT: D 360 MET cc_start: -0.0173 (mmt) cc_final: -0.1768 (mmt) REVERT: D 383 MET cc_start: 0.2783 (ptm) cc_final: 0.2370 (ppp) REVERT: D 474 MET cc_start: -0.1441 (mmp) cc_final: -0.1823 (tmm) REVERT: F 123 MET cc_start: 0.0457 (ttp) cc_final: -0.1617 (ptm) REVERT: F 249 MET cc_start: 0.1439 (ptp) cc_final: 0.0818 (tpp) REVERT: F 297 MET cc_start: 0.0115 (mpp) cc_final: -0.1089 (ttt) REVERT: F 383 MET cc_start: -0.0159 (mtp) cc_final: -0.0750 (tmm) REVERT: F 455 MET cc_start: 0.5227 (mmm) cc_final: 0.3946 (ptp) REVERT: F 480 MET cc_start: 0.2017 (tmm) cc_final: 0.1407 (tmm) outliers start: 65 outliers final: 51 residues processed: 244 average time/residue: 0.1822 time to fit residues: 78.5345 Evaluate side-chains 223 residues out of total 3655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 366 MET Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 51 optimal weight: 7.9990 chunk 317 optimal weight: 6.9990 chunk 234 optimal weight: 0.0970 chunk 400 optimal weight: 40.0000 chunk 403 optimal weight: 30.0000 chunk 161 optimal weight: 0.8980 chunk 224 optimal weight: 30.0000 chunk 381 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 338 optimal weight: 7.9990 chunk 292 optimal weight: 6.9990 overall best weight: 4.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1088 HIS B 370 ASN C 207 HIS F 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.186191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.109726 restraints weight = 92633.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.096933 restraints weight = 87439.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.096061 restraints weight = 72564.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094884 restraints weight = 54935.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093196 restraints weight = 52380.812| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 35220 Z= 0.238 Angle : 0.729 12.412 48064 Z= 0.354 Chirality : 0.049 0.862 5549 Planarity : 0.005 0.053 6036 Dihedral : 5.793 59.506 6404 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.92 % Favored : 93.83 % Rotamer: Outliers : 1.78 % Allowed : 15.27 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 4087 helix: 0.99 (0.14), residues: 1358 sheet: -0.66 (0.20), residues: 584 loop : -1.79 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1019 TYR 0.029 0.002 TYR F 183 PHE 0.032 0.002 PHE C 275 TRP 0.058 0.001 TRP A 104 HIS 0.016 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00538 (35083) covalent geometry : angle 0.70354 (47697) SS BOND : bond 0.00522 ( 44) SS BOND : angle 1.82811 ( 88) hydrogen bonds : bond 0.04537 ( 1312) hydrogen bonds : angle 5.01110 ( 3732) link_BETA1-4 : bond 0.00531 ( 33) link_BETA1-4 : angle 1.85717 ( 99) link_NAG-ASN : bond 0.00646 ( 60) link_NAG-ASN : angle 2.66873 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10732.52 seconds wall clock time: 183 minutes 46.71 seconds (11026.71 seconds total)