Starting phenix.real_space_refine on Fri Mar 6 11:36:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rbv_24403/03_2026/7rbv_24403.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rbv_24403/03_2026/7rbv_24403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rbv_24403/03_2026/7rbv_24403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rbv_24403/03_2026/7rbv_24403.map" model { file = "/net/cci-nas-00/data/ceres_data/7rbv_24403/03_2026/7rbv_24403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rbv_24403/03_2026/7rbv_24403.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.033 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 129 5.16 5 C 19289 2.51 5 N 4905 2.21 5 O 6108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 30431 Number of models: 1 Model: "" Number of chains: 40 Chain: "l" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "h" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "A" Number of atoms: 8474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8474 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 57, 'TRANS': 1026} Chain breaks: 3 Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "B" Number of atoms: 8474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8474 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 57, 'TRANS': 1026} Chain breaks: 3 Chain: "C" Number of atoms: 8474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8474 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 57, 'TRANS': 1026} Chain breaks: 3 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.60, per 1000 atoms: 0.25 Number of scatterers: 30431 At special positions: 0 Unit cell: (151.76, 161.84, 167.44, 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 129 16.00 O 6108 8.00 N 4905 7.00 C 19289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.04 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 97 " distance=2.04 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN F 4 " - " MAN F 5 " " MAN R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-4 " BMA E 3 " - " MAN E 4 " " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1134 " " NAG D 1 " - " ASN A 149 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 137 " " NAG G 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A 61 " " NAG K 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN B 149 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 137 " " NAG S 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 61 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B1074 " " NAG Y 1 " - " ASN B1098 " " NAG Z 1 " - " ASN C 149 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 137 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 61 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 66 sheets defined 19.3% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.592A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.114A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.916A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 418 through 422 removed outlier: 3.660A pdb=" N ASN A 422 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.518A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.588A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.526A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.560A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.726A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 removed outlier: 3.619A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.052A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (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 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.961A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.808A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1146' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.874A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.643A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.183A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.861A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 738 through 744 removed outlier: 3.505A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.566A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.502A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.936A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (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 913 through 919 removed outlier: 3.769A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 removed outlier: 3.636A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.991A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.643A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.043A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.539A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.867A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.897A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.744A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.643A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.023A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 753 " --> pdb=" O CYS C 749 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.585A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.564A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.503A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.574A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.856A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 removed outlier: 3.558A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.838A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 989 through 1033 removed outlier: 3.761A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C1018 " --> pdb=" O ARG C1014 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.585A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'l' and resid 5 through 6 removed outlier: 3.514A pdb=" N CYS l 23 " --> pdb=" O PHE l 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'l' and resid 11 through 13 removed outlier: 3.844A pdb=" N GLU l 105 " --> pdb=" O VAL l 11 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA l 13 " --> pdb=" O GLU l 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR l 85 " --> pdb=" O GLN l 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 5 through 7 removed outlier: 3.597A pdb=" N SER h 7 " --> pdb=" O THR h 21 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR h 21 " --> pdb=" O SER h 7 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU h 20 " --> pdb=" O LEU h 82 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU h 82 " --> pdb=" O LEU h 20 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE h 80 " --> pdb=" O CYS h 22 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN h 79 " --> pdb=" O ASP h 74 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP h 74 " --> pdb=" O GLN h 79 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR h 70 " --> pdb=" O LYS h 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'h' and resid 11 through 12 removed outlier: 3.710A pdb=" N VAL h 12 " --> pdb=" O THR h 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'h' and resid 60 through 61 removed outlier: 5.691A pdb=" N TRP h 49 " --> pdb=" O ARG h 40 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG h 40 " --> pdb=" O TRP h 49 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY h 51 " --> pdb=" O TRP h 38 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP h 38 " --> pdb=" O GLY h 51 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY h 37 " --> pdb=" O ALA h 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE h 39 " --> pdb=" O TYR h 96 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N CYS h 97 " --> pdb=" O TRP h 117 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TRP h 117 " --> pdb=" O CYS h 97 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG h 99 " --> pdb=" O ASP h 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.683A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.683A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.546A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.663A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 135 through 141 removed outlier: 11.453A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.582A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.931A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.764A pdb=" N PHE A 392 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'A' and resid 539 through 541 removed outlier: 3.530A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.039A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.035A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AC1, first strand: chain 'A' and resid 715 through 728 removed outlier: 6.341A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.855A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.547A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC6, first strand: chain 'L' and resid 20 through 22 removed outlier: 3.820A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 34 through 36 removed outlier: 3.956A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL L 104 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.644A pdb=" N LEU H 84 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.561A pdb=" N SER H 81 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER H 72 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR H 70 " --> pdb=" O LYS H 83 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD2, first strand: chain 'H' and resid 36 through 37 removed outlier: 3.574A pdb=" N GLY H 37 " --> pdb=" O ALA H 98 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG H 99 " --> pdb=" O ASP H 115 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 48 through 49 removed outlier: 3.541A pdb=" N ARG H 40 " --> pdb=" O GLU H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 51 through 52 Processing sheet with id=AD5, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.671A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AD7, first strand: chain 'B' and resid 49 through 55 removed outlier: 4.123A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.620A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 135 through 140 removed outlier: 11.905A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.573A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.598A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.845A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.845A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.020A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.571A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.565A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.518A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA B1080 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.523A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.635A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.781A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.781A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.673A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 67 through 68 removed outlier: 3.534A pdb=" N ALA C 67 " --> pdb=" O ALA C 263 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.041A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 118 through 121 removed outlier: 5.375A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.718A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.502A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.516A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG5, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.684A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.234A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 711 through 712 Processing sheet with id=AG8, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.565A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AH1, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.536A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AH3, first strand: chain 'C' and resid 1094 through 1097 791 hydrogen bonds defined for protein. 2097 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: 7.17 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9497 1.35 - 1.47: 8065 1.47 - 1.59: 13403 1.59 - 1.71: 3 1.71 - 1.83: 161 Bond restraints: 31129 Sorted by residual: bond pdb=" C1 MAN R 5 " pdb=" C2 MAN R 5 " ideal model delta sigma weight residual 1.526 1.615 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 MAN b 5 " pdb=" C2 MAN b 5 " ideal model delta sigma weight residual 1.526 1.614 -0.088 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C1 MAN F 5 " pdb=" C2 MAN F 5 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.399 1.483 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 MAN b 5 " pdb=" O5 MAN b 5 " ideal model delta sigma weight residual 1.399 1.480 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 31124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 41784 2.81 - 5.61: 526 5.61 - 8.42: 64 8.42 - 11.22: 3 11.22 - 14.03: 2 Bond angle restraints: 42379 Sorted by residual: angle pdb=" CA ASP A 294 " pdb=" C ASP A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 117.84 124.00 -6.16 1.16e+00 7.43e-01 2.82e+01 angle pdb=" CA ASP A 294 " pdb=" C ASP A 294 " pdb=" O ASP A 294 " ideal model delta sigma weight residual 120.66 115.73 4.93 1.03e+00 9.43e-01 2.29e+01 angle pdb=" CA CYS B 291 " pdb=" C CYS B 291 " pdb=" O CYS B 291 " ideal model delta sigma weight residual 122.13 117.29 4.84 1.13e+00 7.83e-01 1.84e+01 angle pdb=" CA ASP C 294 " pdb=" C ASP C 294 " pdb=" N PRO C 295 " ideal model delta sigma weight residual 117.93 123.78 -5.85 1.42e+00 4.96e-01 1.70e+01 angle pdb=" CA LEU l 47 " pdb=" CB LEU l 47 " pdb=" CG LEU l 47 " ideal model delta sigma weight residual 116.30 130.33 -14.03 3.50e+00 8.16e-02 1.61e+01 ... (remaining 42374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 18336 23.95 - 47.90: 1115 47.90 - 71.85: 199 71.85 - 95.80: 131 95.80 - 119.75: 138 Dihedral angle restraints: 19919 sinusoidal: 9123 harmonic: 10796 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -171.36 85.36 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 164.46 -71.46 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 23.76 69.24 1 1.00e+01 1.00e-02 6.20e+01 ... (remaining 19916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4354 0.067 - 0.135: 670 0.135 - 0.202: 42 0.202 - 0.270: 20 0.270 - 0.337: 10 Chirality restraints: 5096 Sorted by residual: chirality pdb=" CG LEU H 122 " pdb=" CB LEU H 122 " pdb=" CD1 LEU H 122 " pdb=" CD2 LEU H 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 137 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 5093 not shown) Planarity restraints: 5361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 64 " 0.018 2.00e-02 2.50e+03 1.23e-02 3.78e+00 pdb=" CG TRP A 64 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 64 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 64 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 64 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 64 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 64 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 64 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 64 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B1142 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO B1143 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B1143 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B1143 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL l 58 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO l 59 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO l 59 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO l 59 " 0.025 5.00e-02 4.00e+02 ... (remaining 5358 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1493 2.71 - 3.26: 29293 3.26 - 3.81: 44417 3.81 - 4.35: 51338 4.35 - 4.90: 88915 Nonbonded interactions: 215456 Sorted by model distance: nonbonded pdb=" O ASN A 17 " pdb=" OG SER A 254 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR C 674 " pdb=" OE1 GLN C 690 " model vdw 2.193 3.040 nonbonded pdb=" O4 NAG P 2 " pdb=" O7 NAG P 2 " model vdw 2.218 3.040 nonbonded pdb=" O4 NAG Z 2 " pdb=" O7 NAG Z 2 " model vdw 2.228 3.040 nonbonded pdb=" O4 NAG D 2 " pdb=" O7 NAG D 2 " model vdw 2.230 3.040 ... (remaining 215451 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'Q' selection = chain 'R' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'S' selection = chain 'T' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'W' selection = chain 'g' } 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: 25.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.350 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 31283 Z= 0.237 Angle : 0.805 14.025 42798 Z= 0.410 Chirality : 0.050 0.337 5096 Planarity : 0.004 0.046 5313 Dihedral : 19.648 119.754 12872 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.03 % Favored : 91.78 % Rotamer: Outliers : 0.19 % Allowed : 0.52 % Favored : 99.29 % 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: -1.94 (0.13), residues: 3686 helix: -0.11 (0.20), residues: 629 sheet: -0.36 (0.19), residues: 761 loop : -2.08 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 246 TYR 0.021 0.001 TYR h 111 PHE 0.012 0.001 PHE l 71 TRP 0.033 0.001 TRP A 64 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00459 (31129) covalent geometry : angle 0.78979 (42379) SS BOND : bond 0.00406 ( 43) SS BOND : angle 1.22826 ( 86) hydrogen bonds : bond 0.32424 ( 773) hydrogen bonds : angle 8.55359 ( 2097) link_ALPHA1-3 : bond 0.02302 ( 3) link_ALPHA1-3 : angle 2.72693 ( 9) link_ALPHA1-4 : bond 0.00561 ( 3) link_ALPHA1-4 : angle 1.49763 ( 9) link_ALPHA1-6 : bond 0.00482 ( 12) link_ALPHA1-6 : angle 1.52131 ( 36) link_BETA1-4 : bond 0.00752 ( 45) link_BETA1-4 : angle 1.76220 ( 135) link_NAG-ASN : bond 0.00277 ( 48) link_NAG-ASN : angle 2.00500 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 571 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7290 (m-80) cc_final: 0.7067 (m-80) REVERT: A 294 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: B 33 THR cc_start: 0.7545 (p) cc_final: 0.7172 (t) REVERT: B 140 PHE cc_start: 0.7059 (p90) cc_final: 0.6468 (p90) REVERT: B 200 TYR cc_start: 0.6648 (m-80) cc_final: 0.6202 (m-80) REVERT: B 342 PHE cc_start: 0.7727 (m-10) cc_final: 0.7304 (m-80) REVERT: B 365 TYR cc_start: 0.7104 (m-80) cc_final: 0.6634 (m-80) REVERT: B 723 THR cc_start: 0.8990 (m) cc_final: 0.8752 (p) REVERT: B 776 LYS cc_start: 0.8520 (tppp) cc_final: 0.8153 (ttpt) REVERT: B 1118 ASP cc_start: 0.8619 (t0) cc_final: 0.8282 (t0) REVERT: B 1143 PRO cc_start: 0.8959 (Cg_endo) cc_final: 0.8744 (Cg_exo) REVERT: C 64 TRP cc_start: 0.7726 (t60) cc_final: 0.7457 (t60) REVERT: C 189 LEU cc_start: 0.7854 (pp) cc_final: 0.7538 (pp) REVERT: C 319 ARG cc_start: 0.7929 (mmm160) cc_final: 0.7599 (ttm110) REVERT: C 406 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7786 (pt0) REVERT: C 549 THR cc_start: 0.8673 (m) cc_final: 0.8382 (m) REVERT: C 558 LYS cc_start: 0.8285 (mmmm) cc_final: 0.8064 (mptt) REVERT: C 643 PHE cc_start: 0.8466 (t80) cc_final: 0.8253 (t80) REVERT: C 693 ILE cc_start: 0.8313 (mm) cc_final: 0.7962 (pt) REVERT: C 762 GLN cc_start: 0.8743 (tp40) cc_final: 0.8380 (tt0) REVERT: C 776 LYS cc_start: 0.8736 (tppp) cc_final: 0.8306 (ttpp) REVERT: C 1138 TYR cc_start: 0.8160 (t80) cc_final: 0.7934 (t80) outliers start: 6 outliers final: 2 residues processed: 576 average time/residue: 0.2032 time to fit residues: 186.6433 Evaluate side-chains 248 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 6 GLN A 804 GLN L 6 GLN L 55 GLN H 79 GLN B 66 HIS B 196 ASN B 354 ASN B 481 ASN B 901 GLN B1106 GLN C 394 ASN C 563 GLN C1048 HIS C1106 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.170645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130334 restraints weight = 50801.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127792 restraints weight = 92319.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124579 restraints weight = 82792.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122270 restraints weight = 92123.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120120 restraints weight = 86751.580| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 31283 Z= 0.268 Angle : 0.839 10.186 42798 Z= 0.414 Chirality : 0.053 0.301 5096 Planarity : 0.005 0.050 5313 Dihedral : 16.943 105.353 6272 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.17 % Favored : 90.75 % Rotamer: Outliers : 2.41 % Allowed : 12.06 % Favored : 85.54 % 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: -2.03 (0.13), residues: 3686 helix: 0.02 (0.20), residues: 659 sheet: -0.30 (0.18), residues: 843 loop : -2.35 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 101 TYR 0.032 0.002 TYR B 508 PHE 0.027 0.002 PHE C1121 TRP 0.024 0.002 TRP h 49 HIS 0.007 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00655 (31129) covalent geometry : angle 0.81601 (42379) SS BOND : bond 0.00610 ( 43) SS BOND : angle 1.80630 ( 86) hydrogen bonds : bond 0.08762 ( 773) hydrogen bonds : angle 6.11671 ( 2097) link_ALPHA1-3 : bond 0.03803 ( 3) link_ALPHA1-3 : angle 4.08568 ( 9) link_ALPHA1-4 : bond 0.01126 ( 3) link_ALPHA1-4 : angle 3.12569 ( 9) link_ALPHA1-6 : bond 0.00786 ( 12) link_ALPHA1-6 : angle 1.76988 ( 36) link_BETA1-4 : bond 0.00837 ( 45) link_BETA1-4 : angle 2.35786 ( 135) link_NAG-ASN : bond 0.00396 ( 48) link_NAG-ASN : angle 1.96759 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 237 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 19 VAL cc_start: 0.6828 (p) cc_final: 0.6475 (t) REVERT: A 902 MET cc_start: 0.8561 (tpp) cc_final: 0.8282 (tpt) REVERT: A 904 TYR cc_start: 0.7579 (m-10) cc_final: 0.7313 (m-10) REVERT: B 290 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7240 (p0) REVERT: C 549 THR cc_start: 0.9050 (m) cc_final: 0.8814 (m) outliers start: 78 outliers final: 58 residues processed: 304 average time/residue: 0.1859 time to fit residues: 94.3976 Evaluate side-chains 238 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 73 LEU Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 760 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 244 optimal weight: 0.0020 chunk 87 optimal weight: 3.9990 chunk 297 optimal weight: 0.0870 chunk 104 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 300 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 365 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 176 optimal weight: 8.9990 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 89 GLN B 66 HIS B 239 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 957 GLN C 563 GLN C 564 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.174788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.133343 restraints weight = 50953.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130466 restraints weight = 95114.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127923 restraints weight = 89080.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.126754 restraints weight = 88920.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126183 restraints weight = 82522.077| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31283 Z= 0.127 Angle : 0.680 11.293 42798 Z= 0.323 Chirality : 0.047 0.275 5096 Planarity : 0.004 0.042 5313 Dihedral : 14.837 104.845 6269 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.40 % Favored : 93.43 % Rotamer: Outliers : 2.41 % Allowed : 14.22 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.13), residues: 3686 helix: 0.79 (0.21), residues: 658 sheet: -0.08 (0.18), residues: 838 loop : -2.16 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.024 0.001 TYR B 369 PHE 0.030 0.001 PHE l 62 TRP 0.025 0.001 TRP h 49 HIS 0.019 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00253 (31129) covalent geometry : angle 0.65527 (42379) SS BOND : bond 0.00306 ( 43) SS BOND : angle 1.33676 ( 86) hydrogen bonds : bond 0.06046 ( 773) hydrogen bonds : angle 5.44861 ( 2097) link_ALPHA1-3 : bond 0.03390 ( 3) link_ALPHA1-3 : angle 4.19034 ( 9) link_ALPHA1-4 : bond 0.01595 ( 3) link_ALPHA1-4 : angle 2.89486 ( 9) link_ALPHA1-6 : bond 0.00918 ( 12) link_ALPHA1-6 : angle 1.69928 ( 36) link_BETA1-4 : bond 0.00768 ( 45) link_BETA1-4 : angle 2.28890 ( 135) link_NAG-ASN : bond 0.00311 ( 48) link_NAG-ASN : angle 1.70001 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 218 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 19 VAL cc_start: 0.6690 (p) cc_final: 0.6364 (t) REVERT: l 35 TRP cc_start: 0.5678 (m100) cc_final: 0.5452 (m100) REVERT: A 227 VAL cc_start: 0.9019 (p) cc_final: 0.8813 (m) REVERT: B 285 ILE cc_start: 0.7487 (mm) cc_final: 0.7158 (mt) REVERT: B 854 LYS cc_start: 0.6605 (pptt) cc_final: 0.5939 (tptt) REVERT: C 549 THR cc_start: 0.8972 (m) cc_final: 0.8695 (m) outliers start: 78 outliers final: 42 residues processed: 280 average time/residue: 0.1737 time to fit residues: 83.4156 Evaluate side-chains 234 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 48 ILE Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 73 LEU Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 62 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 150 optimal weight: 7.9990 chunk 352 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 92 optimal weight: 0.2980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 79 GLN B 239 GLN B 280 ASN B 460 ASN B 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.170143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128628 restraints weight = 50575.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125103 restraints weight = 88846.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121792 restraints weight = 86749.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119675 restraints weight = 93271.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117694 restraints weight = 84001.586| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31283 Z= 0.201 Angle : 0.746 16.647 42798 Z= 0.356 Chirality : 0.050 0.422 5096 Planarity : 0.004 0.048 5313 Dihedral : 13.211 103.339 6268 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.36 % Favored : 91.51 % Rotamer: Outliers : 3.05 % Allowed : 15.97 % Favored : 80.97 % 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: -1.75 (0.13), residues: 3686 helix: 0.54 (0.21), residues: 665 sheet: -0.13 (0.18), residues: 818 loop : -2.25 (0.12), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 328 TYR 0.033 0.002 TYR B 508 PHE 0.026 0.002 PHE C 157 TRP 0.014 0.001 TRP A 64 HIS 0.006 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00490 (31129) covalent geometry : angle 0.71850 (42379) SS BOND : bond 0.00471 ( 43) SS BOND : angle 1.58763 ( 86) hydrogen bonds : bond 0.07581 ( 773) hydrogen bonds : angle 5.40126 ( 2097) link_ALPHA1-3 : bond 0.03308 ( 3) link_ALPHA1-3 : angle 4.09135 ( 9) link_ALPHA1-4 : bond 0.01924 ( 3) link_ALPHA1-4 : angle 2.77574 ( 9) link_ALPHA1-6 : bond 0.00907 ( 12) link_ALPHA1-6 : angle 1.75068 ( 36) link_BETA1-4 : bond 0.00785 ( 45) link_BETA1-4 : angle 2.36329 ( 135) link_NAG-ASN : bond 0.00350 ( 48) link_NAG-ASN : angle 2.11851 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 191 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 19 VAL cc_start: 0.6922 (p) cc_final: 0.6600 (t) REVERT: l 35 TRP cc_start: 0.5734 (m100) cc_final: 0.5324 (m100) REVERT: l 79 GLN cc_start: 0.6881 (mm110) cc_final: 0.6270 (mt0) REVERT: l 90 GLN cc_start: 0.6461 (OUTLIER) cc_final: 0.6002 (pp30) REVERT: h 50 ILE cc_start: 0.6139 (mp) cc_final: 0.5682 (mt) REVERT: B 140 PHE cc_start: 0.6355 (p90) cc_final: 0.6115 (p90) REVERT: C 549 THR cc_start: 0.9070 (m) cc_final: 0.8823 (m) outliers start: 99 outliers final: 65 residues processed: 280 average time/residue: 0.1668 time to fit residues: 79.5260 Evaluate side-chains 236 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 73 LEU Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 9.9990 chunk 300 optimal weight: 5.9990 chunk 67 optimal weight: 0.0980 chunk 8 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 299 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 89 GLN A1048 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.170479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130495 restraints weight = 51058.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127091 restraints weight = 96082.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123900 restraints weight = 90734.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123003 restraints weight = 93989.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121784 restraints weight = 85182.117| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31283 Z= 0.165 Angle : 0.693 13.706 42798 Z= 0.332 Chirality : 0.048 0.400 5096 Planarity : 0.004 0.041 5313 Dihedral : 12.298 103.325 6268 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.86 % Favored : 93.00 % Rotamer: Outliers : 3.15 % Allowed : 17.11 % Favored : 79.74 % 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: -1.74 (0.13), residues: 3686 helix: 0.61 (0.21), residues: 667 sheet: -0.17 (0.19), residues: 759 loop : -2.19 (0.12), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 328 TYR 0.024 0.001 TYR B 508 PHE 0.029 0.001 PHE C 157 TRP 0.016 0.001 TRP A 64 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00383 (31129) covalent geometry : angle 0.66331 (42379) SS BOND : bond 0.00442 ( 43) SS BOND : angle 1.58483 ( 86) hydrogen bonds : bond 0.06539 ( 773) hydrogen bonds : angle 5.21331 ( 2097) link_ALPHA1-3 : bond 0.03489 ( 3) link_ALPHA1-3 : angle 4.02591 ( 9) link_ALPHA1-4 : bond 0.02342 ( 3) link_ALPHA1-4 : angle 2.66008 ( 9) link_ALPHA1-6 : bond 0.00852 ( 12) link_ALPHA1-6 : angle 1.69479 ( 36) link_BETA1-4 : bond 0.00779 ( 45) link_BETA1-4 : angle 2.27029 ( 135) link_NAG-ASN : bond 0.00339 ( 48) link_NAG-ASN : angle 2.20882 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 182 time to evaluate : 1.133 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: l 19 VAL cc_start: 0.6865 (p) cc_final: 0.6563 (t) REVERT: l 35 TRP cc_start: 0.5691 (m100) cc_final: 0.5401 (m100) REVERT: l 90 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.5980 (pp30) REVERT: h 50 ILE cc_start: 0.6124 (mp) cc_final: 0.5695 (mt) REVERT: B 140 PHE cc_start: 0.6258 (p90) cc_final: 0.6044 (p90) REVERT: B 258 TRP cc_start: 0.5404 (m100) cc_final: 0.5199 (m-90) REVERT: B 854 LYS cc_start: 0.6700 (pptt) cc_final: 0.5974 (tptt) REVERT: C 549 THR cc_start: 0.9060 (m) cc_final: 0.8790 (m) outliers start: 102 outliers final: 71 residues processed: 269 average time/residue: 0.1706 time to fit residues: 79.0779 Evaluate side-chains 247 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 43 optimal weight: 3.9990 chunk 260 optimal weight: 20.0000 chunk 231 optimal weight: 0.3980 chunk 302 optimal weight: 10.0000 chunk 358 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 332 optimal weight: 0.7980 chunk 294 optimal weight: 0.6980 chunk 304 optimal weight: 0.9990 chunk 321 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.172178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.133860 restraints weight = 51125.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130863 restraints weight = 87183.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127019 restraints weight = 77433.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125008 restraints weight = 86202.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123556 restraints weight = 77900.537| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31283 Z= 0.121 Angle : 0.653 12.932 42798 Z= 0.308 Chirality : 0.046 0.427 5096 Planarity : 0.004 0.045 5313 Dihedral : 11.645 101.757 6268 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 2.99 % Allowed : 18.01 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.13), residues: 3686 helix: 0.93 (0.21), residues: 667 sheet: -0.07 (0.19), residues: 754 loop : -2.10 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 457 TYR 0.021 0.001 TYR H 111 PHE 0.032 0.001 PHE C 157 TRP 0.011 0.001 TRP L 35 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00253 (31129) covalent geometry : angle 0.62574 (42379) SS BOND : bond 0.00350 ( 43) SS BOND : angle 1.38572 ( 86) hydrogen bonds : bond 0.05327 ( 773) hydrogen bonds : angle 4.94072 ( 2097) link_ALPHA1-3 : bond 0.03358 ( 3) link_ALPHA1-3 : angle 3.89372 ( 9) link_ALPHA1-4 : bond 0.02392 ( 3) link_ALPHA1-4 : angle 2.46515 ( 9) link_ALPHA1-6 : bond 0.00791 ( 12) link_ALPHA1-6 : angle 1.67150 ( 36) link_BETA1-4 : bond 0.00761 ( 45) link_BETA1-4 : angle 2.25256 ( 135) link_NAG-ASN : bond 0.00275 ( 48) link_NAG-ASN : angle 1.88837 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 187 time to evaluate : 0.930 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: l 19 VAL cc_start: 0.6811 (p) cc_final: 0.6517 (t) REVERT: l 35 TRP cc_start: 0.5670 (m100) cc_final: 0.5379 (m100) REVERT: l 79 GLN cc_start: 0.6576 (mm-40) cc_final: 0.6146 (mt0) REVERT: l 90 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.5747 (pp30) REVERT: h 50 ILE cc_start: 0.6054 (mp) cc_final: 0.5621 (mt) REVERT: B 258 TRP cc_start: 0.5365 (m100) cc_final: 0.5141 (m-90) REVERT: B 854 LYS cc_start: 0.6622 (pptt) cc_final: 0.5891 (tptt) REVERT: C 549 THR cc_start: 0.9032 (m) cc_final: 0.8759 (m) outliers start: 97 outliers final: 71 residues processed: 269 average time/residue: 0.1618 time to fit residues: 75.6138 Evaluate side-chains 247 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 73 LEU Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 363 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 310 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 233 optimal weight: 0.8980 chunk 271 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN B1048 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.171701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.130029 restraints weight = 50711.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126371 restraints weight = 91972.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122985 restraints weight = 82564.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121664 restraints weight = 91047.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120488 restraints weight = 73941.193| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31283 Z= 0.129 Angle : 0.657 11.875 42798 Z= 0.311 Chirality : 0.046 0.434 5096 Planarity : 0.004 0.042 5313 Dihedral : 11.161 98.567 6268 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.70 % Favored : 93.16 % Rotamer: Outliers : 2.78 % Allowed : 18.41 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 3686 helix: 1.02 (0.21), residues: 668 sheet: -0.01 (0.19), residues: 746 loop : -2.08 (0.12), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 328 TYR 0.021 0.001 TYR L 49 PHE 0.032 0.001 PHE C 157 TRP 0.012 0.001 TRP H 38 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00286 (31129) covalent geometry : angle 0.63096 (42379) SS BOND : bond 0.00314 ( 43) SS BOND : angle 1.35591 ( 86) hydrogen bonds : bond 0.05459 ( 773) hydrogen bonds : angle 4.85114 ( 2097) link_ALPHA1-3 : bond 0.03207 ( 3) link_ALPHA1-3 : angle 3.68230 ( 9) link_ALPHA1-4 : bond 0.02409 ( 3) link_ALPHA1-4 : angle 2.40794 ( 9) link_ALPHA1-6 : bond 0.00758 ( 12) link_ALPHA1-6 : angle 1.64727 ( 36) link_BETA1-4 : bond 0.00767 ( 45) link_BETA1-4 : angle 2.24566 ( 135) link_NAG-ASN : bond 0.00267 ( 48) link_NAG-ASN : angle 1.82183 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 185 time to evaluate : 1.370 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: l 19 VAL cc_start: 0.6872 (p) cc_final: 0.6566 (t) REVERT: l 35 TRP cc_start: 0.5674 (m100) cc_final: 0.5403 (m100) REVERT: l 47 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7805 (pp) REVERT: l 79 GLN cc_start: 0.6674 (mm-40) cc_final: 0.6223 (mt0) REVERT: l 90 GLN cc_start: 0.6399 (OUTLIER) cc_final: 0.5761 (pp30) REVERT: h 50 ILE cc_start: 0.6111 (mp) cc_final: 0.5694 (mt) REVERT: B 258 TRP cc_start: 0.5316 (m100) cc_final: 0.5043 (m-90) REVERT: B 854 LYS cc_start: 0.6706 (pptt) cc_final: 0.5872 (tptt) REVERT: C 549 THR cc_start: 0.9066 (m) cc_final: 0.8802 (m) outliers start: 90 outliers final: 71 residues processed: 263 average time/residue: 0.1709 time to fit residues: 77.3651 Evaluate side-chains 246 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 173 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 303 optimal weight: 20.0000 chunk 302 optimal weight: 8.9990 chunk 279 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 19 optimal weight: 50.0000 chunk 75 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 180 optimal weight: 0.0070 chunk 342 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 79 GLN L 89 GLN C 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.166771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126945 restraints weight = 51028.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124212 restraints weight = 91413.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121021 restraints weight = 88813.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119886 restraints weight = 90268.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117296 restraints weight = 82834.811| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 31283 Z= 0.258 Angle : 0.791 14.315 42798 Z= 0.385 Chirality : 0.051 0.451 5096 Planarity : 0.005 0.065 5313 Dihedral : 11.081 98.080 6268 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.22 % Favored : 90.64 % Rotamer: Outliers : 3.36 % Allowed : 18.75 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.13), residues: 3686 helix: 0.33 (0.21), residues: 665 sheet: -0.16 (0.19), residues: 739 loop : -2.22 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 905 TYR 0.018 0.002 TYR A 170 PHE 0.029 0.002 PHE C 374 TRP 0.023 0.002 TRP A 64 HIS 0.008 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00637 (31129) covalent geometry : angle 0.76407 (42379) SS BOND : bond 0.00618 ( 43) SS BOND : angle 2.03260 ( 86) hydrogen bonds : bond 0.08545 ( 773) hydrogen bonds : angle 5.42988 ( 2097) link_ALPHA1-3 : bond 0.03210 ( 3) link_ALPHA1-3 : angle 3.66381 ( 9) link_ALPHA1-4 : bond 0.02242 ( 3) link_ALPHA1-4 : angle 2.42774 ( 9) link_ALPHA1-6 : bond 0.00824 ( 12) link_ALPHA1-6 : angle 1.60337 ( 36) link_BETA1-4 : bond 0.00841 ( 45) link_BETA1-4 : angle 2.39228 ( 135) link_NAG-ASN : bond 0.00394 ( 48) link_NAG-ASN : angle 2.14972 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 180 time to evaluate : 1.184 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: l 19 VAL cc_start: 0.6909 (p) cc_final: 0.6622 (t) REVERT: l 35 TRP cc_start: 0.5704 (m100) cc_final: 0.5464 (m100) REVERT: l 47 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7808 (pp) REVERT: l 90 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.5595 (pp30) REVERT: h 50 ILE cc_start: 0.6078 (mp) cc_final: 0.5669 (mt) REVERT: A 1029 MET cc_start: 0.8961 (tpp) cc_final: 0.8652 (ttm) REVERT: B 140 PHE cc_start: 0.6222 (p90) cc_final: 0.5960 (p90) REVERT: B 258 TRP cc_start: 0.5446 (m100) cc_final: 0.5201 (m-90) REVERT: B 854 LYS cc_start: 0.6853 (pptt) cc_final: 0.6007 (tptt) REVERT: B 977 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8567 (mp) REVERT: C 990 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7409 (mp0) outliers start: 109 outliers final: 78 residues processed: 274 average time/residue: 0.1764 time to fit residues: 83.0242 Evaluate side-chains 253 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 171 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 20 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 184 optimal weight: 8.9990 chunk 301 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 153 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 chunk 216 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.168472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.129060 restraints weight = 51123.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.126351 restraints weight = 90137.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122754 restraints weight = 82593.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120975 restraints weight = 93011.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119273 restraints weight = 81484.541| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31283 Z= 0.171 Angle : 0.708 11.296 42798 Z= 0.340 Chirality : 0.048 0.435 5096 Planarity : 0.004 0.058 5313 Dihedral : 10.705 97.422 6268 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.30 % Favored : 92.57 % Rotamer: Outliers : 2.71 % Allowed : 19.43 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.13), residues: 3686 helix: 0.56 (0.21), residues: 665 sheet: -0.12 (0.19), residues: 748 loop : -2.21 (0.12), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 457 TYR 0.020 0.001 TYR B 421 PHE 0.032 0.001 PHE C 157 TRP 0.018 0.001 TRP A 64 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00405 (31129) covalent geometry : angle 0.68011 (42379) SS BOND : bond 0.00460 ( 43) SS BOND : angle 1.69178 ( 86) hydrogen bonds : bond 0.06632 ( 773) hydrogen bonds : angle 5.12277 ( 2097) link_ALPHA1-3 : bond 0.03286 ( 3) link_ALPHA1-3 : angle 3.68618 ( 9) link_ALPHA1-4 : bond 0.02414 ( 3) link_ALPHA1-4 : angle 2.41544 ( 9) link_ALPHA1-6 : bond 0.00739 ( 12) link_ALPHA1-6 : angle 1.58781 ( 36) link_BETA1-4 : bond 0.00789 ( 45) link_BETA1-4 : angle 2.34477 ( 135) link_NAG-ASN : bond 0.00309 ( 48) link_NAG-ASN : angle 2.00905 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 185 time to evaluate : 1.173 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: l 19 VAL cc_start: 0.6941 (p) cc_final: 0.6652 (t) REVERT: l 47 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7823 (pp) REVERT: h 50 ILE cc_start: 0.6096 (mp) cc_final: 0.5708 (mt) REVERT: B 140 PHE cc_start: 0.6243 (p90) cc_final: 0.5960 (p90) REVERT: B 258 TRP cc_start: 0.5433 (m100) cc_final: 0.5190 (m-90) REVERT: B 854 LYS cc_start: 0.6720 (pptt) cc_final: 0.5923 (tptt) REVERT: C 990 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7373 (mp0) outliers start: 88 outliers final: 75 residues processed: 261 average time/residue: 0.1646 time to fit residues: 73.0570 Evaluate side-chains 252 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 175 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 20 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 276 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 353 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 236 optimal weight: 0.7980 chunk 59 optimal weight: 0.0470 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.168898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129421 restraints weight = 50769.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126552 restraints weight = 90332.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123671 restraints weight = 81309.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122230 restraints weight = 82687.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120261 restraints weight = 81385.688| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31283 Z= 0.152 Angle : 0.697 11.365 42798 Z= 0.334 Chirality : 0.047 0.428 5096 Planarity : 0.004 0.052 5313 Dihedral : 10.303 96.815 6268 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.33 % Favored : 91.48 % Rotamer: Outliers : 2.50 % Allowed : 19.83 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.13), residues: 3686 helix: 0.69 (0.21), residues: 665 sheet: -0.12 (0.19), residues: 780 loop : -2.18 (0.12), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 634 TYR 0.021 0.001 TYR B 421 PHE 0.033 0.001 PHE C 157 TRP 0.022 0.001 TRP l 32 HIS 0.003 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00354 (31129) covalent geometry : angle 0.66925 (42379) SS BOND : bond 0.00444 ( 43) SS BOND : angle 1.66235 ( 86) hydrogen bonds : bond 0.06252 ( 773) hydrogen bonds : angle 5.02302 ( 2097) link_ALPHA1-3 : bond 0.03181 ( 3) link_ALPHA1-3 : angle 3.58254 ( 9) link_ALPHA1-4 : bond 0.02255 ( 3) link_ALPHA1-4 : angle 2.45647 ( 9) link_ALPHA1-6 : bond 0.00717 ( 12) link_ALPHA1-6 : angle 1.59528 ( 36) link_BETA1-4 : bond 0.00780 ( 45) link_BETA1-4 : angle 2.31650 ( 135) link_NAG-ASN : bond 0.00295 ( 48) link_NAG-ASN : angle 2.02193 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 172 time to evaluate : 1.103 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: l 19 VAL cc_start: 0.6927 (p) cc_final: 0.6650 (t) REVERT: l 47 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7821 (pp) REVERT: h 50 ILE cc_start: 0.6038 (mp) cc_final: 0.5650 (mt) REVERT: B 140 PHE cc_start: 0.6200 (p90) cc_final: 0.5996 (p90) REVERT: B 258 TRP cc_start: 0.5475 (m100) cc_final: 0.5208 (m-90) REVERT: B 854 LYS cc_start: 0.6687 (pptt) cc_final: 0.5860 (tptt) REVERT: C 990 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7358 (mp0) outliers start: 81 outliers final: 74 residues processed: 241 average time/residue: 0.1610 time to fit residues: 67.5442 Evaluate side-chains 245 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 169 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 20 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 131 optimal weight: 0.4980 chunk 290 optimal weight: 2.9990 chunk 308 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 181 optimal weight: 0.6980 chunk 267 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 354 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.168973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127492 restraints weight = 51043.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123893 restraints weight = 91381.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120270 restraints weight = 87023.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119156 restraints weight = 87266.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117351 restraints weight = 78643.930| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31283 Z= 0.152 Angle : 0.682 10.823 42798 Z= 0.326 Chirality : 0.046 0.405 5096 Planarity : 0.004 0.055 5313 Dihedral : 9.919 96.499 6268 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.68 % Favored : 92.13 % Rotamer: Outliers : 2.50 % Allowed : 20.01 % Favored : 77.49 % 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: -1.65 (0.13), residues: 3686 helix: 0.72 (0.21), residues: 667 sheet: -0.13 (0.19), residues: 785 loop : -2.16 (0.12), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 634 TYR 0.018 0.001 TYR B 421 PHE 0.033 0.001 PHE C 157 TRP 0.020 0.001 TRP l 32 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00354 (31129) covalent geometry : angle 0.65271 (42379) SS BOND : bond 0.00432 ( 43) SS BOND : angle 1.55813 ( 86) hydrogen bonds : bond 0.06150 ( 773) hydrogen bonds : angle 4.96432 ( 2097) link_ALPHA1-3 : bond 0.03203 ( 3) link_ALPHA1-3 : angle 3.56584 ( 9) link_ALPHA1-4 : bond 0.02238 ( 3) link_ALPHA1-4 : angle 2.49396 ( 9) link_ALPHA1-6 : bond 0.00707 ( 12) link_ALPHA1-6 : angle 1.58581 ( 36) link_BETA1-4 : bond 0.00771 ( 45) link_BETA1-4 : angle 2.24814 ( 135) link_NAG-ASN : bond 0.00308 ( 48) link_NAG-ASN : angle 2.17766 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5716.24 seconds wall clock time: 99 minutes 42.10 seconds (5982.10 seconds total)