Starting phenix.real_space_refine on Fri Mar 6 04:00:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sbp_24984/03_2026/7sbp_24984.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbp_24984/03_2026/7sbp_24984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sbp_24984/03_2026/7sbp_24984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbp_24984/03_2026/7sbp_24984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sbp_24984/03_2026/7sbp_24984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbp_24984/03_2026/7sbp_24984.map" } resolution = 3.1 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= 0.042 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 117 5.16 5 C 17553 2.51 5 N 4461 2.21 5 O 5562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 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: 27693 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8688 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 53, 'TRANS': 1056} Chain breaks: 4 Chain: "B" Number of atoms: 8688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8688 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 53, 'TRANS': 1056} Chain breaks: 4 Chain: "C" Number of atoms: 8688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8688 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 53, 'TRANS': 1056} Chain breaks: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: {'MAN': 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: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.11, per 1000 atoms: 0.22 Number of scatterers: 27693 At special positions: 0 Unit cell: (150.162, 146.862, 196.366, 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 117 16.00 O 5562 8.00 N 4461 7.00 C 17553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.99 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 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 ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " " NAG G 2 " - " MAN G 3 " " NAG I 2 " - " MAN I 3 " " NAG J 2 " - " MAN J 3 " " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG O 2 " - " MAN O 3 " " NAG Q 2 " - " MAN Q 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG Z 2 " - " MAN Z 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG e 2 " - " MAN e 3 " " NAG g 2 " - " MAN g 3 " " NAG h 2 " - " MAN h 3 " " NAG j 2 " - " MAN j 3 " " NAG k 2 " - " MAN k 3 " " NAG l 2 " - " MAN l 3 " " NAG m 2 " - " MAN m 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " BETA1-6 " NAG K 1 " - " FUC K 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG i 1 " - " FUC i 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 343 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 282 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN B 165 " " NAG a 1 " - " ASN B 343 " " NAG b 1 " - " ASN C 17 " " NAG c 1 " - " ASN C 122 " " NAG d 1 " - " ASN C 234 " " NAG e 1 " - " ASN C 282 " " NAG f 1 " - " ASN C 616 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " " NAG k 1 " - " ASN C1134 " " NAG l 1 " - " ASN C 165 " " NAG m 1 " - " ASN C 343 " Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 47 sheets defined 27.3% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.861A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.972A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.187A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.580A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.510A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.787A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.620A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.714A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 4.425A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.532A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.450A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.800A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.242A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.789A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.839A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.750A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.834A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.473A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 4.118A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.044A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.466A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 843 through 848 removed outlier: 4.282A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.647A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.298A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.921A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1160 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.719A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.951A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.240A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.858A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.977A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.936A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.631A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 846 removed outlier: 3.605A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 846 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.876A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.574A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.542A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.793A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 removed outlier: 3.564A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.083A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1159 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.915A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.901A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.937A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.302A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.392A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 7.040A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.956A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.661A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.508A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.874A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.953A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.577A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.009A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.843A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.926A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.685A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.185A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.146A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.961A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.229A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.579A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.529A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.945A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.262A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.440A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.005A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.642A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.967A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 134 through 145 removed outlier: 8.054A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.122A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 7.048A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.045A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.735A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.876A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.570A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 2967 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4438 1.30 - 1.43: 7441 1.43 - 1.56: 16279 1.56 - 1.69: 0 1.69 - 1.82: 144 Bond restraints: 28302 Sorted by residual: bond pdb=" C PRO C 217 " pdb=" N HIS C 218 " ideal model delta sigma weight residual 1.331 1.245 0.086 1.42e-02 4.96e+03 3.63e+01 bond pdb=" C TYR A 279 " pdb=" O TYR A 279 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.22e-02 6.72e+03 2.78e+01 bond pdb=" C ARG A 328 " pdb=" O ARG A 328 " ideal model delta sigma weight residual 1.234 1.178 0.057 1.11e-02 8.12e+03 2.62e+01 bond pdb=" C ARG B1019 " pdb=" O ARG B1019 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.16e-02 7.43e+03 2.51e+01 bond pdb=" C ARG C1019 " pdb=" O ARG C1019 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.19e-02 7.06e+03 2.45e+01 ... (remaining 28297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 33013 2.61 - 5.22: 5215 5.22 - 7.83: 263 7.83 - 10.44: 15 10.44 - 13.05: 2 Bond angle restraints: 38508 Sorted by residual: angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 108.38 121.43 -13.05 1.35e+00 5.49e-01 9.34e+01 angle pdb=" N ARG B1107 " pdb=" CA ARG B1107 " pdb=" C ARG B1107 " ideal model delta sigma weight residual 112.38 122.72 -10.34 1.22e+00 6.72e-01 7.18e+01 angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 113.20 102.98 10.22 1.21e+00 6.83e-01 7.14e+01 angle pdb=" C GLY B 526 " pdb=" N PRO B 527 " pdb=" CA PRO B 527 " ideal model delta sigma weight residual 120.83 128.09 -7.26 1.02e+00 9.61e-01 5.06e+01 angle pdb=" N PRO C 217 " pdb=" CA PRO C 217 " pdb=" C PRO C 217 " ideal model delta sigma weight residual 111.15 121.68 -10.53 1.58e+00 4.01e-01 4.44e+01 ... (remaining 38503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 17548 25.61 - 51.23: 585 51.23 - 76.84: 164 76.84 - 102.46: 59 102.46 - 128.07: 70 Dihedral angle restraints: 18426 sinusoidal: 8724 harmonic: 9702 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -168.49 82.49 1 1.00e+01 1.00e-02 8.35e+01 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 -165.22 79.22 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" C LEU C 24 " pdb=" N LEU C 24 " pdb=" CA LEU C 24 " pdb=" CB LEU C 24 " ideal model delta harmonic sigma weight residual -122.60 -143.79 21.19 0 2.50e+00 1.60e-01 7.18e+01 ... (remaining 18423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.271: 4651 0.271 - 0.542: 56 0.542 - 0.813: 7 0.813 - 1.084: 0 1.084 - 1.355: 2 Chirality restraints: 4716 Sorted by residual: chirality pdb=" C1 MAN F 3 " pdb=" O4 NAG F 2 " pdb=" C2 MAN F 3 " pdb=" O5 MAN F 3 " both_signs ideal model delta sigma weight residual False 2.40 2.16 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 MAN O 3 " pdb=" O4 NAG O 2 " pdb=" C2 MAN O 3 " pdb=" O5 MAN O 3 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-02 2.50e+03 7.09e+01 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.66e+01 ... (remaining 4713 not shown) Planarity restraints: 4860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 104 " -0.186 2.00e-02 2.50e+03 9.85e-02 2.43e+02 pdb=" CG TRP C 104 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP C 104 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP C 104 " 0.097 2.00e-02 2.50e+03 pdb=" NE1 TRP C 104 " 0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP C 104 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP C 104 " 0.139 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 104 " -0.112 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 104 " 0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP C 104 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " -0.097 2.00e-02 2.50e+03 1.11e-01 1.54e+02 pdb=" CG ASN B 122 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " 0.182 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.099 2.00e-02 2.50e+03 9.98e-02 1.25e+02 pdb=" CG ASN A1134 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.146 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.121 2.00e-02 2.50e+03 ... (remaining 4857 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 192 2.64 - 3.21: 24650 3.21 - 3.77: 41212 3.77 - 4.34: 58914 4.34 - 4.90: 93951 Nonbonded interactions: 218919 Sorted by model distance: nonbonded pdb=" O ARG C 634 " pdb=" NH1 ARG C 634 " model vdw 2.078 3.120 nonbonded pdb=" NH1 ARG C 905 " pdb=" O LEU C1049 " model vdw 2.214 3.120 nonbonded pdb=" NH1 ARG B 905 " pdb=" O LEU B1049 " model vdw 2.228 3.120 nonbonded pdb=" OG SER C 349 " pdb=" O ARG C 452 " model vdw 2.230 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.247 3.040 ... (remaining 218914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'P' selection = chain 'T' selection = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.650 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 : 0.015 0.086 28470 Z= 0.802 Angle : 1.838 23.166 38967 Z= 1.173 Chirality : 0.110 1.355 4716 Planarity : 0.012 0.125 4803 Dihedral : 17.092 128.074 12051 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.03 % Favored : 92.30 % Rotamer: Outliers : 1.38 % Allowed : 5.27 % Favored : 93.35 % Cbeta Deviations : 0.48 % 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: 3300 helix: -1.19 (0.16), residues: 747 sheet: -0.33 (0.18), residues: 738 loop : -1.64 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 44 TYR 0.119 0.021 TYR C 660 PHE 0.105 0.013 PHE C 133 TRP 0.186 0.032 TRP C 104 HIS 0.014 0.003 HIS A1159 Details of bonding type rmsd covalent geometry : bond 0.01453 (28302) covalent geometry : angle 1.78940 (38508) SS BOND : bond 0.01213 ( 45) SS BOND : angle 2.38578 ( 90) hydrogen bonds : bond 0.16351 ( 1092) hydrogen bonds : angle 8.48825 ( 2967) link_ALPHA1-4 : bond 0.02447 ( 27) link_ALPHA1-4 : angle 3.58772 ( 81) link_BETA1-4 : bond 0.02311 ( 36) link_BETA1-4 : angle 3.96410 ( 108) link_BETA1-6 : bond 0.02987 ( 3) link_BETA1-6 : angle 3.20640 ( 9) link_NAG-ASN : bond 0.01132 ( 57) link_NAG-ASN : angle 5.42523 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 787 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8257 (mttt) cc_final: 0.8007 (mtmm) REVERT: A 52 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 81 ASN cc_start: 0.8879 (m-40) cc_final: 0.8380 (m-40) REVERT: A 237 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7307 (mtm-85) REVERT: A 319 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.8133 (ttm110) REVERT: A 351 TYR cc_start: 0.8303 (p90) cc_final: 0.7986 (p90) REVERT: A 354 ASN cc_start: 0.8222 (t0) cc_final: 0.7963 (t0) REVERT: A 396 TYR cc_start: 0.7840 (m-80) cc_final: 0.7270 (m-80) REVERT: A 421 TYR cc_start: 0.7516 (m-80) cc_final: 0.6958 (m-10) REVERT: A 462 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8334 (mmmm) REVERT: A 495 TYR cc_start: 0.7937 (m-80) cc_final: 0.7706 (m-80) REVERT: A 540 ASN cc_start: 0.8366 (m-40) cc_final: 0.8165 (m-40) REVERT: A 555 SER cc_start: 0.8926 (t) cc_final: 0.8465 (p) REVERT: A 565 PHE cc_start: 0.7475 (m-80) cc_final: 0.7028 (m-80) REVERT: A 574 ASP cc_start: 0.8018 (p0) cc_final: 0.7757 (p0) REVERT: A 578 ASP cc_start: 0.6928 (m-30) cc_final: 0.6305 (m-30) REVERT: A 584 ILE cc_start: 0.9073 (mm) cc_final: 0.8708 (mm) REVERT: A 585 LEU cc_start: 0.7957 (mt) cc_final: 0.7648 (mt) REVERT: A 596 SER cc_start: 0.8827 (m) cc_final: 0.8506 (p) REVERT: A 643 PHE cc_start: 0.8183 (t80) cc_final: 0.7796 (t80) REVERT: A 658 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8191 (p0) REVERT: A 663 ASP cc_start: 0.7985 (t0) cc_final: 0.7684 (t0) REVERT: A 702 GLU cc_start: 0.8242 (tp30) cc_final: 0.7922 (tp30) REVERT: A 708 SER cc_start: 0.9022 (t) cc_final: 0.8694 (p) REVERT: A 736 VAL cc_start: 0.9082 (t) cc_final: 0.8865 (m) REVERT: A 758 SER cc_start: 0.8295 (t) cc_final: 0.8079 (t) REVERT: A 788 ILE cc_start: 0.9131 (mm) cc_final: 0.8787 (mm) REVERT: A 796 ASP cc_start: 0.7990 (t0) cc_final: 0.7719 (t0) REVERT: A 912 THR cc_start: 0.9022 (m) cc_final: 0.8714 (p) REVERT: A 986 LYS cc_start: 0.8329 (ttmm) cc_final: 0.8106 (ttpt) REVERT: A 994 ASP cc_start: 0.8035 (t70) cc_final: 0.7704 (t0) REVERT: A 1100 THR cc_start: 0.8987 (m) cc_final: 0.8757 (p) REVERT: B 58 PHE cc_start: 0.9170 (m-10) cc_final: 0.8868 (m-80) REVERT: B 140 PHE cc_start: 0.7779 (p90) cc_final: 0.7560 (p90) REVERT: B 191 GLU cc_start: 0.7542 (pt0) cc_final: 0.7289 (pt0) REVERT: B 287 ASP cc_start: 0.7917 (t0) cc_final: 0.7595 (t0) REVERT: B 298 GLU cc_start: 0.8109 (tt0) cc_final: 0.7562 (tm-30) REVERT: B 301 CYS cc_start: 0.6950 (t) cc_final: 0.6274 (t) REVERT: B 319 ARG cc_start: 0.8463 (ttp-110) cc_final: 0.8196 (ptm-80) REVERT: B 369 TYR cc_start: 0.7030 (t80) cc_final: 0.6821 (t80) REVERT: B 396 TYR cc_start: 0.7965 (m-80) cc_final: 0.7301 (m-10) REVERT: B 462 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8518 (mtmm) REVERT: B 465 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7538 (mt-10) REVERT: B 490 PHE cc_start: 0.8339 (t80) cc_final: 0.8094 (t80) REVERT: B 574 ASP cc_start: 0.7913 (p0) cc_final: 0.7712 (p0) REVERT: B 596 SER cc_start: 0.9078 (m) cc_final: 0.8828 (m) REVERT: B 738 CYS cc_start: 0.5870 (t) cc_final: 0.5534 (t) REVERT: B 762 GLN cc_start: 0.8047 (tt0) cc_final: 0.7819 (tt0) REVERT: B 790 LYS cc_start: 0.8711 (ptpp) cc_final: 0.8433 (ptmt) REVERT: B 796 ASP cc_start: 0.7988 (t0) cc_final: 0.7656 (t0) REVERT: B 808 ASP cc_start: 0.7909 (t0) cc_final: 0.7671 (t0) REVERT: B 814 LYS cc_start: 0.8516 (mmtm) cc_final: 0.8226 (mptt) REVERT: B 985 ASP cc_start: 0.7777 (p0) cc_final: 0.7360 (p0) REVERT: B 994 ASP cc_start: 0.7974 (t70) cc_final: 0.7608 (t0) REVERT: B 1005 GLN cc_start: 0.7636 (mt0) cc_final: 0.7418 (mt0) REVERT: B 1073 LYS cc_start: 0.8591 (mttm) cc_final: 0.8377 (mttm) REVERT: B 1149 LYS cc_start: 0.8777 (tmtt) cc_final: 0.8486 (tppp) REVERT: C 54 LEU cc_start: 0.8753 (mt) cc_final: 0.8537 (mt) REVERT: C 116 SER cc_start: 0.8742 (m) cc_final: 0.8387 (p) REVERT: C 135 PHE cc_start: 0.7065 (m-80) cc_final: 0.6517 (m-80) REVERT: C 191 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7131 (mt-10) REVERT: C 342 PHE cc_start: 0.8438 (m-80) cc_final: 0.8192 (m-80) REVERT: C 360 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8165 (t0) REVERT: C 402 ILE cc_start: 0.8531 (pt) cc_final: 0.8258 (pt) REVERT: C 420 ASP cc_start: 0.7427 (m-30) cc_final: 0.7085 (m-30) REVERT: C 436 TRP cc_start: 0.8174 (p90) cc_final: 0.7850 (p90) REVERT: C 455 LEU cc_start: 0.8249 (tp) cc_final: 0.8012 (mt) REVERT: C 462 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8511 (mmmm) REVERT: C 512 VAL cc_start: 0.9320 (t) cc_final: 0.9007 (m) REVERT: C 563 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8163 (mm-40) REVERT: C 581 THR cc_start: 0.8922 (p) cc_final: 0.8606 (t) REVERT: C 583 GLU cc_start: 0.7315 (mp0) cc_final: 0.7114 (mp0) REVERT: C 586 ASP cc_start: 0.8194 (t70) cc_final: 0.7860 (t0) REVERT: C 737 ASP cc_start: 0.7512 (t0) cc_final: 0.7232 (t0) REVERT: C 776 LYS cc_start: 0.8624 (tttm) cc_final: 0.8245 (tttm) REVERT: C 780 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7470 (mm-30) REVERT: C 796 ASP cc_start: 0.7974 (t0) cc_final: 0.7495 (t0) REVERT: C 817 PHE cc_start: 0.8715 (t80) cc_final: 0.8341 (t80) REVERT: C 907 ASN cc_start: 0.8692 (t0) cc_final: 0.8409 (t0) REVERT: C 912 THR cc_start: 0.8784 (m) cc_final: 0.8435 (p) REVERT: C 935 GLN cc_start: 0.8630 (tp-100) cc_final: 0.7797 (tp-100) REVERT: C 985 ASP cc_start: 0.7585 (p0) cc_final: 0.7353 (p0) REVERT: C 994 ASP cc_start: 0.7905 (t70) cc_final: 0.7607 (t0) REVERT: C 1101 ASP cc_start: 0.7425 (m-30) cc_final: 0.7195 (m-30) outliers start: 40 outliers final: 13 residues processed: 814 average time/residue: 0.1940 time to fit residues: 241.4289 Evaluate side-chains 668 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 652 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 843 ASP Chi-restraints excluded: chain C residue 1014 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1119 ASN B 125 ASN B 450 ASN B 658 ASN B 955 ASN B 969 ASN B1002 GLN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS C 370 ASN C 394 ASN C 580 GLN C 675 GLN C 960 ASN C1005 GLN C1108 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.111382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.088670 restraints weight = 61397.742| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.61 r_work: 0.3216 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28470 Z= 0.192 Angle : 0.831 10.432 38967 Z= 0.403 Chirality : 0.048 0.255 4716 Planarity : 0.004 0.052 4803 Dihedral : 14.795 114.334 6129 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 2.17 % Allowed : 9.96 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3300 helix: 0.76 (0.19), residues: 753 sheet: -0.22 (0.18), residues: 762 loop : -1.24 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 452 TYR 0.022 0.002 TYR C 495 PHE 0.024 0.002 PHE C 497 TRP 0.021 0.002 TRP B 64 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00427 (28302) covalent geometry : angle 0.79003 (38508) SS BOND : bond 0.00612 ( 45) SS BOND : angle 2.31039 ( 90) hydrogen bonds : bond 0.04850 ( 1092) hydrogen bonds : angle 6.28526 ( 2967) link_ALPHA1-4 : bond 0.01289 ( 27) link_ALPHA1-4 : angle 2.58283 ( 81) link_BETA1-4 : bond 0.00311 ( 36) link_BETA1-4 : angle 1.71129 ( 108) link_BETA1-6 : bond 0.01292 ( 3) link_BETA1-6 : angle 1.66247 ( 9) link_NAG-ASN : bond 0.00577 ( 57) link_NAG-ASN : angle 2.96271 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 656 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.8112 (m) cc_final: 0.7892 (m) REVERT: A 32 PHE cc_start: 0.8208 (m-80) cc_final: 0.7938 (m-80) REVERT: A 41 LYS cc_start: 0.8358 (mttt) cc_final: 0.7991 (mtmm) REVERT: A 190 ARG cc_start: 0.7549 (tpp80) cc_final: 0.7064 (tpp80) REVERT: A 207 HIS cc_start: 0.7982 (p90) cc_final: 0.7252 (p-80) REVERT: A 237 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.8133 (mtm-85) REVERT: A 242 LEU cc_start: 0.8094 (mt) cc_final: 0.7839 (mt) REVERT: A 271 GLN cc_start: 0.8180 (mp10) cc_final: 0.7680 (mp10) REVERT: A 287 ASP cc_start: 0.8366 (t0) cc_final: 0.8063 (m-30) REVERT: A 317 ASN cc_start: 0.8693 (p0) cc_final: 0.8202 (p0) REVERT: A 319 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8417 (ttm110) REVERT: A 351 TYR cc_start: 0.8660 (p90) cc_final: 0.8238 (p90) REVERT: A 408 ARG cc_start: 0.8522 (ptm-80) cc_final: 0.8239 (ptm-80) REVERT: A 565 PHE cc_start: 0.7695 (m-80) cc_final: 0.7380 (m-80) REVERT: A 586 ASP cc_start: 0.8737 (t70) cc_final: 0.8297 (t0) REVERT: A 591 SER cc_start: 0.7878 (t) cc_final: 0.7506 (t) REVERT: A 643 PHE cc_start: 0.8323 (t80) cc_final: 0.7958 (t80) REVERT: A 658 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8217 (p0) REVERT: A 663 ASP cc_start: 0.8345 (t0) cc_final: 0.8053 (t0) REVERT: A 736 VAL cc_start: 0.9119 (t) cc_final: 0.8776 (m) REVERT: A 737 ASP cc_start: 0.7971 (p0) cc_final: 0.7611 (p0) REVERT: A 796 ASP cc_start: 0.8482 (t0) cc_final: 0.8207 (t0) REVERT: A 804 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8521 (tp40) REVERT: A 994 ASP cc_start: 0.8652 (t70) cc_final: 0.8332 (t0) REVERT: A 1072 GLU cc_start: 0.8365 (pm20) cc_final: 0.8101 (pm20) REVERT: A 1119 ASN cc_start: 0.8580 (m110) cc_final: 0.8301 (m-40) REVERT: B 140 PHE cc_start: 0.8462 (p90) cc_final: 0.8119 (p90) REVERT: B 187 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7662 (mmtt) REVERT: B 281 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8265 (pp20) REVERT: B 287 ASP cc_start: 0.8342 (t0) cc_final: 0.8042 (m-30) REVERT: B 319 ARG cc_start: 0.8784 (ttp-110) cc_final: 0.8368 (ptm-80) REVERT: B 351 TYR cc_start: 0.8731 (p90) cc_final: 0.8295 (p90) REVERT: B 369 TYR cc_start: 0.7689 (t80) cc_final: 0.7358 (t80) REVERT: B 389 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7702 (t0) REVERT: B 396 TYR cc_start: 0.8244 (m-80) cc_final: 0.8014 (m-10) REVERT: B 455 LEU cc_start: 0.8770 (tp) cc_final: 0.8542 (mt) REVERT: B 462 LYS cc_start: 0.8931 (mmtm) cc_final: 0.8576 (mtmm) REVERT: B 465 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8084 (mt-10) REVERT: B 490 PHE cc_start: 0.8283 (t80) cc_final: 0.7890 (t80) REVERT: B 523 THR cc_start: 0.8250 (p) cc_final: 0.7723 (t) REVERT: B 568 ASP cc_start: 0.8446 (t0) cc_final: 0.8204 (t0) REVERT: B 578 ASP cc_start: 0.8379 (t0) cc_final: 0.8037 (t70) REVERT: B 661 GLU cc_start: 0.7695 (pm20) cc_final: 0.7461 (pm20) REVERT: B 796 ASP cc_start: 0.8511 (t0) cc_final: 0.8099 (t0) REVERT: B 808 ASP cc_start: 0.8054 (t0) cc_final: 0.7707 (t0) REVERT: B 994 ASP cc_start: 0.8642 (t70) cc_final: 0.8374 (t0) REVERT: B 1072 GLU cc_start: 0.8579 (pm20) cc_final: 0.8125 (pm20) REVERT: C 52 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8577 (tm-30) REVERT: C 132 GLU cc_start: 0.7220 (tp30) cc_final: 0.6913 (tp30) REVERT: C 191 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7860 (mt-10) REVERT: C 195 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8398 (ttmm) REVERT: C 278 LYS cc_start: 0.8706 (tttt) cc_final: 0.8388 (ttpt) REVERT: C 298 GLU cc_start: 0.8728 (tp30) cc_final: 0.8514 (tp30) REVERT: C 351 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8554 (p90) REVERT: C 360 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8334 (t0) REVERT: C 402 ILE cc_start: 0.8441 (pt) cc_final: 0.8201 (pt) REVERT: C 448 ASN cc_start: 0.7976 (t0) cc_final: 0.7558 (t0) REVERT: C 450 ASN cc_start: 0.8846 (m110) cc_final: 0.8428 (p0) REVERT: C 462 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8433 (mmmm) REVERT: C 466 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7778 (ptp90) REVERT: C 563 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8008 (mm-40) REVERT: C 564 GLN cc_start: 0.8375 (tp40) cc_final: 0.7992 (tp40) REVERT: C 586 ASP cc_start: 0.8581 (t70) cc_final: 0.8381 (t0) REVERT: C 643 PHE cc_start: 0.8304 (t80) cc_final: 0.7993 (t80) REVERT: C 758 SER cc_start: 0.8343 (t) cc_final: 0.8089 (t) REVERT: C 776 LYS cc_start: 0.8941 (tttm) cc_final: 0.8639 (tttm) REVERT: C 780 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8130 (mm-30) REVERT: C 787 GLN cc_start: 0.8576 (mt0) cc_final: 0.8359 (mp10) REVERT: C 796 ASP cc_start: 0.8407 (t0) cc_final: 0.8012 (t0) REVERT: C 912 THR cc_start: 0.8767 (m) cc_final: 0.8481 (p) REVERT: C 935 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8329 (tt0) REVERT: C 994 ASP cc_start: 0.8663 (t70) cc_final: 0.8284 (t0) REVERT: C 1101 ASP cc_start: 0.8142 (m-30) cc_final: 0.7940 (m-30) REVERT: C 1119 ASN cc_start: 0.8869 (m-40) cc_final: 0.8561 (m-40) outliers start: 63 outliers final: 31 residues processed: 694 average time/residue: 0.1835 time to fit residues: 197.6693 Evaluate side-chains 622 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 583 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 215 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 257 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 804 GLN A1005 GLN B 66 HIS B 207 HIS B 388 ASN B 655 HIS B 658 ASN B 919 ASN B1010 GLN C 66 HIS C 563 GLN C1002 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.109094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086740 restraints weight = 61290.082| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.53 r_work: 0.3192 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 28470 Z= 0.248 Angle : 0.816 11.465 38967 Z= 0.393 Chirality : 0.048 0.285 4716 Planarity : 0.005 0.062 4803 Dihedral : 14.024 113.623 6113 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.91 % Favored : 94.88 % Rotamer: Outliers : 3.00 % Allowed : 12.24 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3300 helix: 1.35 (0.19), residues: 747 sheet: -0.08 (0.19), residues: 714 loop : -1.27 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.022 0.002 TYR C1067 PHE 0.026 0.002 PHE B 643 TRP 0.034 0.002 TRP B 64 HIS 0.011 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00558 (28302) covalent geometry : angle 0.77663 (38508) SS BOND : bond 0.00576 ( 45) SS BOND : angle 2.58877 ( 90) hydrogen bonds : bond 0.04641 ( 1092) hydrogen bonds : angle 6.00915 ( 2967) link_ALPHA1-4 : bond 0.01511 ( 27) link_ALPHA1-4 : angle 2.65429 ( 81) link_BETA1-4 : bond 0.00237 ( 36) link_BETA1-4 : angle 1.54941 ( 108) link_BETA1-6 : bond 0.01145 ( 3) link_BETA1-6 : angle 1.59394 ( 9) link_NAG-ASN : bond 0.00447 ( 57) link_NAG-ASN : angle 2.71959 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 608 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7529 (tpp80) cc_final: 0.6871 (tpp80) REVERT: A 242 LEU cc_start: 0.8150 (mt) cc_final: 0.7815 (mt) REVERT: A 271 GLN cc_start: 0.8211 (mp10) cc_final: 0.7616 (mp10) REVERT: A 319 ARG cc_start: 0.8672 (ttp-110) cc_final: 0.8382 (ttm110) REVERT: A 351 TYR cc_start: 0.8740 (p90) cc_final: 0.8297 (p90) REVERT: A 353 TRP cc_start: 0.8513 (p-90) cc_final: 0.8155 (p-90) REVERT: A 398 ASP cc_start: 0.7331 (m-30) cc_final: 0.6795 (m-30) REVERT: A 408 ARG cc_start: 0.8565 (ptm-80) cc_final: 0.8339 (ptm-80) REVERT: A 565 PHE cc_start: 0.7741 (m-80) cc_final: 0.7467 (m-80) REVERT: A 568 ASP cc_start: 0.8455 (t0) cc_final: 0.8229 (t0) REVERT: A 574 ASP cc_start: 0.8347 (p0) cc_final: 0.8081 (p0) REVERT: A 586 ASP cc_start: 0.8784 (t70) cc_final: 0.8403 (t0) REVERT: A 591 SER cc_start: 0.7921 (t) cc_final: 0.7576 (t) REVERT: A 643 PHE cc_start: 0.8429 (t80) cc_final: 0.7950 (t80) REVERT: A 658 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8326 (p0) REVERT: A 790 LYS cc_start: 0.8978 (ptpp) cc_final: 0.8493 (ptpp) REVERT: A 796 ASP cc_start: 0.8531 (t0) cc_final: 0.8272 (t0) REVERT: A 994 ASP cc_start: 0.8666 (t70) cc_final: 0.8343 (t0) REVERT: A 1092 GLU cc_start: 0.7903 (mp0) cc_final: 0.7688 (mp0) REVERT: A 1119 ASN cc_start: 0.8617 (m110) cc_final: 0.8349 (m-40) REVERT: B 140 PHE cc_start: 0.8485 (p90) cc_final: 0.8180 (p90) REVERT: B 190 ARG cc_start: 0.7521 (tpp-160) cc_final: 0.6939 (tpp-160) REVERT: B 281 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8249 (pp20) REVERT: B 287 ASP cc_start: 0.8375 (t0) cc_final: 0.8059 (m-30) REVERT: B 319 ARG cc_start: 0.8811 (ttp-110) cc_final: 0.8302 (ptm-80) REVERT: B 351 TYR cc_start: 0.8761 (p90) cc_final: 0.8282 (p90) REVERT: B 369 TYR cc_start: 0.7755 (t80) cc_final: 0.7384 (t80) REVERT: B 389 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7837 (t0) REVERT: B 460 ASN cc_start: 0.8376 (m-40) cc_final: 0.8119 (m-40) REVERT: B 490 PHE cc_start: 0.8314 (t80) cc_final: 0.7920 (t80) REVERT: B 523 THR cc_start: 0.8398 (p) cc_final: 0.7855 (t) REVERT: B 578 ASP cc_start: 0.8425 (t0) cc_final: 0.8046 (t70) REVERT: B 591 SER cc_start: 0.8961 (t) cc_final: 0.8662 (p) REVERT: B 661 GLU cc_start: 0.7733 (pm20) cc_final: 0.7470 (pm20) REVERT: B 758 SER cc_start: 0.8555 (t) cc_final: 0.8325 (p) REVERT: B 796 ASP cc_start: 0.8583 (t0) cc_final: 0.8163 (t0) REVERT: B 808 ASP cc_start: 0.8089 (t0) cc_final: 0.7748 (t0) REVERT: B 994 ASP cc_start: 0.8680 (t70) cc_final: 0.8418 (t0) REVERT: B 1073 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8385 (mttm) REVERT: C 132 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: C 153 MET cc_start: 0.6099 (mpp) cc_final: 0.5702 (mpp) REVERT: C 191 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7565 (mp0) REVERT: C 278 LYS cc_start: 0.8808 (tttt) cc_final: 0.8476 (ttpt) REVERT: C 298 GLU cc_start: 0.8753 (tp30) cc_final: 0.8460 (tp30) REVERT: C 347 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.6582 (m-80) REVERT: C 360 ASN cc_start: 0.8775 (t0) cc_final: 0.8449 (t0) REVERT: C 368 LEU cc_start: 0.9116 (pp) cc_final: 0.8861 (pp) REVERT: C 402 ILE cc_start: 0.8539 (pt) cc_final: 0.7657 (pt) REVERT: C 406 GLU cc_start: 0.7451 (pm20) cc_final: 0.7058 (pm20) REVERT: C 462 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8590 (mmmm) REVERT: C 516 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: C 564 GLN cc_start: 0.8455 (tp40) cc_final: 0.8009 (tp40) REVERT: C 578 ASP cc_start: 0.8112 (t0) cc_final: 0.7813 (t70) REVERT: C 643 PHE cc_start: 0.8335 (t80) cc_final: 0.8023 (t80) REVERT: C 776 LYS cc_start: 0.8901 (tttm) cc_final: 0.8526 (tttm) REVERT: C 780 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8131 (mm-30) REVERT: C 787 GLN cc_start: 0.8645 (mt0) cc_final: 0.8433 (mt0) REVERT: C 796 ASP cc_start: 0.8484 (t0) cc_final: 0.8132 (t0) REVERT: C 935 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8356 (tt0) REVERT: C 994 ASP cc_start: 0.8678 (t70) cc_final: 0.8237 (t0) REVERT: C 1073 LYS cc_start: 0.8819 (mttp) cc_final: 0.8587 (mtpp) REVERT: C 1119 ASN cc_start: 0.8891 (m-40) cc_final: 0.8535 (m-40) outliers start: 87 outliers final: 46 residues processed: 656 average time/residue: 0.1870 time to fit residues: 189.7605 Evaluate side-chains 623 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 571 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 986 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 260 optimal weight: 0.8980 chunk 303 optimal weight: 0.0270 chunk 40 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 188 optimal weight: 0.0050 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 327 optimal weight: 0.7980 chunk 257 optimal weight: 0.9990 overall best weight: 0.4852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 360 ASN A 388 ASN A 658 ASN A1005 GLN B 66 HIS B 658 ASN B1005 GLN C 66 HIS C1002 GLN C1159 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.111361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.089045 restraints weight = 60551.082| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.56 r_work: 0.3234 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28470 Z= 0.143 Angle : 0.751 10.912 38967 Z= 0.355 Chirality : 0.046 0.252 4716 Planarity : 0.004 0.101 4803 Dihedral : 12.934 110.988 6101 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.00 % Favored : 95.79 % Rotamer: Outliers : 2.79 % Allowed : 13.62 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3300 helix: 1.74 (0.19), residues: 747 sheet: -0.13 (0.19), residues: 714 loop : -1.09 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 403 TYR 0.021 0.001 TYR B 396 PHE 0.020 0.001 PHE A 65 TRP 0.025 0.001 TRP B 64 HIS 0.026 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00309 (28302) covalent geometry : angle 0.71308 (38508) SS BOND : bond 0.00508 ( 45) SS BOND : angle 2.47478 ( 90) hydrogen bonds : bond 0.03954 ( 1092) hydrogen bonds : angle 5.80984 ( 2967) link_ALPHA1-4 : bond 0.01544 ( 27) link_ALPHA1-4 : angle 2.79656 ( 81) link_BETA1-4 : bond 0.00346 ( 36) link_BETA1-4 : angle 1.35098 ( 108) link_BETA1-6 : bond 0.01260 ( 3) link_BETA1-6 : angle 1.84234 ( 9) link_NAG-ASN : bond 0.00386 ( 57) link_NAG-ASN : angle 2.38507 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 604 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6886 (mtt-85) cc_final: 0.6630 (mtt-85) REVERT: A 134 GLN cc_start: 0.8180 (tp-100) cc_final: 0.7928 (tp-100) REVERT: A 158 ARG cc_start: 0.7270 (mmt-90) cc_final: 0.6299 (mmt-90) REVERT: A 242 LEU cc_start: 0.8054 (mt) cc_final: 0.7544 (mt) REVERT: A 269 TYR cc_start: 0.7575 (m-10) cc_final: 0.7329 (m-10) REVERT: A 271 GLN cc_start: 0.8182 (mp10) cc_final: 0.7517 (mp10) REVERT: A 298 GLU cc_start: 0.8763 (tp30) cc_final: 0.8453 (tp30) REVERT: A 319 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8342 (ttm110) REVERT: A 351 TYR cc_start: 0.8704 (p90) cc_final: 0.8304 (p90) REVERT: A 353 TRP cc_start: 0.8462 (p-90) cc_final: 0.8109 (p-90) REVERT: A 398 ASP cc_start: 0.7354 (m-30) cc_final: 0.6740 (m-30) REVERT: A 490 PHE cc_start: 0.8307 (t80) cc_final: 0.7826 (t80) REVERT: A 505 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: A 565 PHE cc_start: 0.7727 (m-80) cc_final: 0.7429 (m-80) REVERT: A 568 ASP cc_start: 0.8327 (t0) cc_final: 0.8097 (t0) REVERT: A 574 ASP cc_start: 0.8321 (p0) cc_final: 0.8066 (p0) REVERT: A 585 LEU cc_start: 0.8992 (mt) cc_final: 0.8725 (mt) REVERT: A 643 PHE cc_start: 0.8359 (t80) cc_final: 0.7868 (t80) REVERT: A 790 LYS cc_start: 0.8964 (ptpp) cc_final: 0.8603 (ptpp) REVERT: A 796 ASP cc_start: 0.8536 (t0) cc_final: 0.8312 (t0) REVERT: A 804 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8714 (mp10) REVERT: A 994 ASP cc_start: 0.8609 (t70) cc_final: 0.8278 (t0) REVERT: A 1119 ASN cc_start: 0.8533 (m110) cc_final: 0.8247 (m-40) REVERT: B 65 PHE cc_start: 0.8865 (m-80) cc_final: 0.8642 (m-80) REVERT: B 140 PHE cc_start: 0.8445 (p90) cc_final: 0.8114 (p90) REVERT: B 191 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: B 207 HIS cc_start: 0.8256 (t-90) cc_final: 0.7181 (t70) REVERT: B 281 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8478 (pp20) REVERT: B 287 ASP cc_start: 0.8311 (t0) cc_final: 0.8023 (m-30) REVERT: B 319 ARG cc_start: 0.8818 (ttp-110) cc_final: 0.8468 (ttm110) REVERT: B 341 VAL cc_start: 0.9077 (m) cc_final: 0.8845 (p) REVERT: B 351 TYR cc_start: 0.8700 (p90) cc_final: 0.8273 (p90) REVERT: B 389 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7665 (t0) REVERT: B 403 ARG cc_start: 0.7780 (ttp-110) cc_final: 0.7563 (mtm110) REVERT: B 460 ASN cc_start: 0.8504 (m-40) cc_final: 0.8252 (m-40) REVERT: B 465 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7629 (mt-10) REVERT: B 490 PHE cc_start: 0.8354 (t80) cc_final: 0.8009 (t80) REVERT: B 523 THR cc_start: 0.8410 (p) cc_final: 0.7859 (t) REVERT: B 578 ASP cc_start: 0.8450 (t0) cc_final: 0.8097 (t70) REVERT: B 661 GLU cc_start: 0.7619 (pm20) cc_final: 0.7255 (pm20) REVERT: B 776 LYS cc_start: 0.8916 (ttmm) cc_final: 0.8637 (tttt) REVERT: B 796 ASP cc_start: 0.8574 (t0) cc_final: 0.8191 (t0) REVERT: B 808 ASP cc_start: 0.8105 (t0) cc_final: 0.7716 (t0) REVERT: B 994 ASP cc_start: 0.8653 (t70) cc_final: 0.8338 (t0) REVERT: B 1073 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8313 (mttm) REVERT: C 146 HIS cc_start: 0.6414 (m-70) cc_final: 0.6132 (m170) REVERT: C 158 ARG cc_start: 0.6954 (mtt180) cc_final: 0.6445 (mtt180) REVERT: C 191 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7585 (mp0) REVERT: C 192 PHE cc_start: 0.8188 (m-80) cc_final: 0.7979 (m-10) REVERT: C 278 LYS cc_start: 0.8828 (tttt) cc_final: 0.8493 (ttpt) REVERT: C 298 GLU cc_start: 0.8759 (tp30) cc_final: 0.8520 (tp30) REVERT: C 346 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7613 (tpp80) REVERT: C 347 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: C 351 TYR cc_start: 0.8769 (p90) cc_final: 0.8292 (p90) REVERT: C 360 ASN cc_start: 0.8750 (t0) cc_final: 0.8432 (t0) REVERT: C 368 LEU cc_start: 0.9068 (pp) cc_final: 0.8792 (pp) REVERT: C 448 ASN cc_start: 0.7847 (t0) cc_final: 0.7572 (t0) REVERT: C 462 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8594 (mmmm) REVERT: C 564 GLN cc_start: 0.8423 (tp40) cc_final: 0.8086 (tp-100) REVERT: C 578 ASP cc_start: 0.8181 (t0) cc_final: 0.7928 (t70) REVERT: C 643 PHE cc_start: 0.8280 (t80) cc_final: 0.7966 (t80) REVERT: C 776 LYS cc_start: 0.8882 (tttm) cc_final: 0.8552 (tttm) REVERT: C 780 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8125 (mm-30) REVERT: C 787 GLN cc_start: 0.8632 (mt0) cc_final: 0.8422 (mt0) REVERT: C 796 ASP cc_start: 0.8425 (t0) cc_final: 0.8135 (t0) REVERT: C 994 ASP cc_start: 0.8593 (t70) cc_final: 0.8159 (t0) REVERT: C 1072 GLU cc_start: 0.8378 (pm20) cc_final: 0.8113 (pm20) REVERT: C 1073 LYS cc_start: 0.8777 (mttp) cc_final: 0.8534 (mtpp) REVERT: C 1119 ASN cc_start: 0.8855 (m-40) cc_final: 0.8433 (m-40) outliers start: 81 outliers final: 36 residues processed: 659 average time/residue: 0.1831 time to fit residues: 188.4085 Evaluate side-chains 607 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 565 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 293 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 314 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 249 optimal weight: 0.6980 chunk 220 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 804 GLN A 935 GLN A1002 GLN A1005 GLN A1088 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B1005 GLN B1088 HIS C 66 HIS C 804 GLN C1159 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.110340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087708 restraints weight = 61061.958| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.62 r_work: 0.3212 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28470 Z= 0.170 Angle : 0.745 11.567 38967 Z= 0.350 Chirality : 0.046 0.268 4716 Planarity : 0.004 0.068 4803 Dihedral : 12.299 110.706 6099 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.48 % Favored : 95.33 % Rotamer: Outliers : 2.86 % Allowed : 14.00 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3300 helix: 1.96 (0.20), residues: 732 sheet: -0.14 (0.19), residues: 714 loop : -1.06 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1091 TYR 0.019 0.001 TYR C1067 PHE 0.025 0.001 PHE C 168 TRP 0.021 0.001 TRP A 104 HIS 0.025 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00379 (28302) covalent geometry : angle 0.70794 (38508) SS BOND : bond 0.00504 ( 45) SS BOND : angle 2.37723 ( 90) hydrogen bonds : bond 0.03956 ( 1092) hydrogen bonds : angle 5.67642 ( 2967) link_ALPHA1-4 : bond 0.01609 ( 27) link_ALPHA1-4 : angle 2.83199 ( 81) link_BETA1-4 : bond 0.00272 ( 36) link_BETA1-4 : angle 1.33188 ( 108) link_BETA1-6 : bond 0.01197 ( 3) link_BETA1-6 : angle 1.92784 ( 9) link_NAG-ASN : bond 0.00363 ( 57) link_NAG-ASN : angle 2.36851 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 591 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6820 (mtt-85) cc_final: 0.6529 (mtt-85) REVERT: A 158 ARG cc_start: 0.7309 (mmt-90) cc_final: 0.7017 (mmt-90) REVERT: A 220 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.8110 (t80) REVERT: A 242 LEU cc_start: 0.8031 (mt) cc_final: 0.7485 (mt) REVERT: A 271 GLN cc_start: 0.8270 (mp10) cc_final: 0.7877 (mp10) REVERT: A 298 GLU cc_start: 0.8780 (tp30) cc_final: 0.8456 (tp30) REVERT: A 319 ARG cc_start: 0.8690 (ttp-110) cc_final: 0.8414 (ttm110) REVERT: A 351 TYR cc_start: 0.8729 (p90) cc_final: 0.8339 (p90) REVERT: A 353 TRP cc_start: 0.8488 (p-90) cc_final: 0.8112 (p-90) REVERT: A 398 ASP cc_start: 0.7453 (m-30) cc_final: 0.6788 (m-30) REVERT: A 505 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: A 565 PHE cc_start: 0.7750 (m-80) cc_final: 0.7454 (m-80) REVERT: A 574 ASP cc_start: 0.8315 (p0) cc_final: 0.8094 (p0) REVERT: A 585 LEU cc_start: 0.8990 (mt) cc_final: 0.8775 (mt) REVERT: A 643 PHE cc_start: 0.8340 (t80) cc_final: 0.7820 (t80) REVERT: A 725 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: A 790 LYS cc_start: 0.8993 (ptpp) cc_final: 0.8588 (ptpp) REVERT: A 796 ASP cc_start: 0.8537 (t0) cc_final: 0.8325 (t0) REVERT: A 994 ASP cc_start: 0.8621 (t70) cc_final: 0.8307 (t0) REVERT: A 1119 ASN cc_start: 0.8551 (m110) cc_final: 0.8313 (m-40) REVERT: B 54 LEU cc_start: 0.9046 (mm) cc_final: 0.8813 (mt) REVERT: B 65 PHE cc_start: 0.8806 (m-80) cc_final: 0.8582 (m-80) REVERT: B 140 PHE cc_start: 0.8443 (p90) cc_final: 0.8118 (p90) REVERT: B 191 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: B 207 HIS cc_start: 0.8208 (t-90) cc_final: 0.7493 (t-90) REVERT: B 281 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8461 (pp20) REVERT: B 287 ASP cc_start: 0.8322 (t0) cc_final: 0.8030 (m-30) REVERT: B 319 ARG cc_start: 0.8733 (ttp-110) cc_final: 0.8501 (ttm110) REVERT: B 341 VAL cc_start: 0.9123 (m) cc_final: 0.8913 (p) REVERT: B 351 TYR cc_start: 0.8758 (p90) cc_final: 0.8273 (p90) REVERT: B 374 PHE cc_start: 0.8351 (m-80) cc_final: 0.8134 (m-80) REVERT: B 389 ASP cc_start: 0.8053 (t0) cc_final: 0.7695 (t0) REVERT: B 490 PHE cc_start: 0.8420 (t80) cc_final: 0.8097 (t80) REVERT: B 523 THR cc_start: 0.8503 (p) cc_final: 0.7967 (t) REVERT: B 578 ASP cc_start: 0.8443 (t0) cc_final: 0.8106 (t70) REVERT: B 661 GLU cc_start: 0.7714 (pm20) cc_final: 0.7325 (pm20) REVERT: B 796 ASP cc_start: 0.8596 (t0) cc_final: 0.8220 (t0) REVERT: B 808 ASP cc_start: 0.8159 (t0) cc_final: 0.7789 (t0) REVERT: B 994 ASP cc_start: 0.8688 (t70) cc_final: 0.8373 (t0) REVERT: B 1073 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8305 (mttm) REVERT: B 1082 CYS cc_start: 0.7206 (t) cc_final: 0.6926 (t) REVERT: C 132 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6781 (tp30) REVERT: C 191 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7590 (mp0) REVERT: C 192 PHE cc_start: 0.8165 (m-80) cc_final: 0.7964 (m-10) REVERT: C 278 LYS cc_start: 0.8854 (tttt) cc_final: 0.8526 (ttpt) REVERT: C 298 GLU cc_start: 0.8808 (tp30) cc_final: 0.8539 (tp30) REVERT: C 347 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6626 (m-80) REVERT: C 360 ASN cc_start: 0.8803 (t0) cc_final: 0.8498 (t0) REVERT: C 368 LEU cc_start: 0.9085 (pp) cc_final: 0.8773 (pp) REVERT: C 462 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8655 (mmmm) REVERT: C 516 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: C 564 GLN cc_start: 0.8476 (tp40) cc_final: 0.8119 (tp40) REVERT: C 578 ASP cc_start: 0.8196 (t0) cc_final: 0.7932 (t70) REVERT: C 643 PHE cc_start: 0.8227 (t80) cc_final: 0.7959 (t80) REVERT: C 776 LYS cc_start: 0.8888 (tttm) cc_final: 0.8615 (tttm) REVERT: C 780 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8153 (mm-30) REVERT: C 787 GLN cc_start: 0.8680 (mt0) cc_final: 0.8462 (mt0) REVERT: C 794 ILE cc_start: 0.9041 (mm) cc_final: 0.8826 (tp) REVERT: C 796 ASP cc_start: 0.8473 (t0) cc_final: 0.8205 (t0) REVERT: C 994 ASP cc_start: 0.8646 (t70) cc_final: 0.8222 (t0) REVERT: C 1072 GLU cc_start: 0.8431 (pm20) cc_final: 0.8162 (pm20) REVERT: C 1119 ASN cc_start: 0.8863 (m-40) cc_final: 0.8464 (m-40) outliers start: 83 outliers final: 50 residues processed: 640 average time/residue: 0.1872 time to fit residues: 186.7916 Evaluate side-chains 621 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 564 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 191 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 291 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 360 ASN A 388 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 207 HIS B 388 ASN B 658 ASN B 804 GLN B1005 GLN C1002 GLN C1088 HIS C1159 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.087619 restraints weight = 60948.209| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.60 r_work: 0.3220 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28470 Z= 0.169 Angle : 0.746 15.608 38967 Z= 0.349 Chirality : 0.046 0.277 4716 Planarity : 0.004 0.063 4803 Dihedral : 11.563 111.422 6098 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.42 % Favored : 95.39 % Rotamer: Outliers : 2.76 % Allowed : 14.96 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3300 helix: 1.98 (0.20), residues: 732 sheet: -0.06 (0.19), residues: 714 loop : -1.08 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1091 TYR 0.026 0.001 TYR A1138 PHE 0.021 0.001 PHE C 392 TRP 0.028 0.001 TRP A 104 HIS 0.012 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00374 (28302) covalent geometry : angle 0.71057 (38508) SS BOND : bond 0.00415 ( 45) SS BOND : angle 2.16510 ( 90) hydrogen bonds : bond 0.03930 ( 1092) hydrogen bonds : angle 5.61941 ( 2967) link_ALPHA1-4 : bond 0.01657 ( 27) link_ALPHA1-4 : angle 2.97378 ( 81) link_BETA1-4 : bond 0.00279 ( 36) link_BETA1-4 : angle 1.29451 ( 108) link_BETA1-6 : bond 0.01182 ( 3) link_BETA1-6 : angle 2.04546 ( 9) link_NAG-ASN : bond 0.00354 ( 57) link_NAG-ASN : angle 2.31096 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 599 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6788 (mtt-85) cc_final: 0.6500 (mtt-85) REVERT: A 158 ARG cc_start: 0.7301 (mmt-90) cc_final: 0.6988 (mmt-90) REVERT: A 191 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7521 (mp0) REVERT: A 220 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8085 (t80) REVERT: A 242 LEU cc_start: 0.7963 (mt) cc_final: 0.7550 (mt) REVERT: A 269 TYR cc_start: 0.7616 (m-10) cc_final: 0.7347 (m-10) REVERT: A 271 GLN cc_start: 0.8269 (mp10) cc_final: 0.7544 (mp10) REVERT: A 278 LYS cc_start: 0.8981 (tttt) cc_final: 0.8709 (ttmt) REVERT: A 298 GLU cc_start: 0.8768 (tp30) cc_final: 0.8441 (tp30) REVERT: A 319 ARG cc_start: 0.8720 (ttp-110) cc_final: 0.8447 (ttm110) REVERT: A 351 TYR cc_start: 0.8720 (p90) cc_final: 0.8362 (p90) REVERT: A 353 TRP cc_start: 0.8436 (p-90) cc_final: 0.8041 (p-90) REVERT: A 398 ASP cc_start: 0.7477 (m-30) cc_final: 0.6749 (m-30) REVERT: A 490 PHE cc_start: 0.8407 (t80) cc_final: 0.7930 (t80) REVERT: A 505 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: A 523 THR cc_start: 0.8550 (p) cc_final: 0.8209 (t) REVERT: A 565 PHE cc_start: 0.7743 (m-80) cc_final: 0.7447 (m-80) REVERT: A 586 ASP cc_start: 0.8630 (t70) cc_final: 0.8416 (t0) REVERT: A 725 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: A 808 ASP cc_start: 0.8091 (t0) cc_final: 0.7873 (t0) REVERT: A 994 ASP cc_start: 0.8621 (t70) cc_final: 0.8319 (t0) REVERT: A 995 ARG cc_start: 0.8838 (mtt-85) cc_final: 0.8598 (mtp180) REVERT: A 1107 ARG cc_start: 0.8464 (mtt90) cc_final: 0.8191 (mtt90) REVERT: A 1119 ASN cc_start: 0.8574 (m110) cc_final: 0.8325 (m-40) REVERT: B 65 PHE cc_start: 0.8793 (m-80) cc_final: 0.8537 (m-80) REVERT: B 140 PHE cc_start: 0.8383 (p90) cc_final: 0.8066 (p90) REVERT: B 191 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: B 207 HIS cc_start: 0.7971 (t70) cc_final: 0.7477 (t-90) REVERT: B 281 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8444 (pp20) REVERT: B 287 ASP cc_start: 0.8346 (t0) cc_final: 0.7968 (m-30) REVERT: B 298 GLU cc_start: 0.8667 (tt0) cc_final: 0.7965 (tm-30) REVERT: B 319 ARG cc_start: 0.8748 (ttp-110) cc_final: 0.8539 (ttm110) REVERT: B 351 TYR cc_start: 0.8783 (p90) cc_final: 0.8294 (p90) REVERT: B 389 ASP cc_start: 0.8024 (t0) cc_final: 0.7671 (t0) REVERT: B 490 PHE cc_start: 0.8445 (t80) cc_final: 0.8115 (t80) REVERT: B 523 THR cc_start: 0.8541 (p) cc_final: 0.7969 (t) REVERT: B 578 ASP cc_start: 0.8467 (t0) cc_final: 0.8158 (t70) REVERT: B 661 GLU cc_start: 0.7766 (pm20) cc_final: 0.7432 (pm20) REVERT: B 796 ASP cc_start: 0.8585 (t0) cc_final: 0.8236 (t0) REVERT: B 808 ASP cc_start: 0.8110 (t0) cc_final: 0.7749 (t0) REVERT: B 817 PHE cc_start: 0.8760 (t80) cc_final: 0.8175 (t80) REVERT: B 934 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8838 (tt) REVERT: B 986 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8106 (mmmt) REVERT: B 990 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: B 994 ASP cc_start: 0.8682 (t70) cc_final: 0.8266 (t0) REVERT: B 1072 GLU cc_start: 0.8607 (pm20) cc_final: 0.8224 (pm20) REVERT: B 1073 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8311 (mttm) REVERT: B 1082 CYS cc_start: 0.7187 (t) cc_final: 0.6916 (t) REVERT: C 191 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7644 (mp0) REVERT: C 278 LYS cc_start: 0.8884 (tttt) cc_final: 0.8547 (ttpt) REVERT: C 298 GLU cc_start: 0.8784 (tp30) cc_final: 0.8533 (tp30) REVERT: C 347 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: C 360 ASN cc_start: 0.8817 (t0) cc_final: 0.8529 (t0) REVERT: C 368 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8843 (pp) REVERT: C 461 LEU cc_start: 0.9141 (tp) cc_final: 0.8925 (tt) REVERT: C 462 LYS cc_start: 0.9042 (mmmt) cc_final: 0.8755 (mmmm) REVERT: C 564 GLN cc_start: 0.8507 (tp40) cc_final: 0.8145 (tp40) REVERT: C 578 ASP cc_start: 0.8196 (t0) cc_final: 0.7939 (t70) REVERT: C 643 PHE cc_start: 0.8199 (t80) cc_final: 0.7910 (t80) REVERT: C 710 ASN cc_start: 0.9114 (p0) cc_final: 0.8882 (p0) REVERT: C 776 LYS cc_start: 0.8887 (tttm) cc_final: 0.8599 (tttm) REVERT: C 780 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8181 (mm-30) REVERT: C 787 GLN cc_start: 0.8693 (mt0) cc_final: 0.8280 (mt0) REVERT: C 790 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8758 (mtmt) REVERT: C 794 ILE cc_start: 0.9041 (mm) cc_final: 0.8825 (tp) REVERT: C 796 ASP cc_start: 0.8465 (t0) cc_final: 0.8208 (t0) REVERT: C 814 LYS cc_start: 0.8586 (mmpt) cc_final: 0.8362 (mptt) REVERT: C 994 ASP cc_start: 0.8645 (t70) cc_final: 0.8194 (t0) REVERT: C 1072 GLU cc_start: 0.8449 (pm20) cc_final: 0.8180 (pm20) REVERT: C 1092 GLU cc_start: 0.8254 (pm20) cc_final: 0.7888 (pm20) REVERT: C 1119 ASN cc_start: 0.8891 (m-40) cc_final: 0.8494 (m-40) outliers start: 80 outliers final: 50 residues processed: 649 average time/residue: 0.1798 time to fit residues: 181.7822 Evaluate side-chains 632 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 572 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 253 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 658 ASN B 804 GLN B1005 GLN C 188 ASN C 394 ASN C1159 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.110398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087889 restraints weight = 60445.654| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.58 r_work: 0.3234 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28470 Z= 0.162 Angle : 0.747 15.439 38967 Z= 0.349 Chirality : 0.045 0.277 4716 Planarity : 0.004 0.054 4803 Dihedral : 10.969 111.377 6098 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.00 % Favored : 95.82 % Rotamer: Outliers : 2.83 % Allowed : 15.55 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3300 helix: 2.04 (0.20), residues: 732 sheet: -0.12 (0.19), residues: 717 loop : -1.00 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1091 TYR 0.019 0.001 TYR C1067 PHE 0.022 0.001 PHE C 392 TRP 0.030 0.001 TRP A 104 HIS 0.012 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00359 (28302) covalent geometry : angle 0.71086 (38508) SS BOND : bond 0.00445 ( 45) SS BOND : angle 2.29887 ( 90) hydrogen bonds : bond 0.03806 ( 1092) hydrogen bonds : angle 5.58237 ( 2967) link_ALPHA1-4 : bond 0.01696 ( 27) link_ALPHA1-4 : angle 2.92216 ( 81) link_BETA1-4 : bond 0.00290 ( 36) link_BETA1-4 : angle 1.28419 ( 108) link_BETA1-6 : bond 0.01199 ( 3) link_BETA1-6 : angle 2.17360 ( 9) link_NAG-ASN : bond 0.00350 ( 57) link_NAG-ASN : angle 2.26202 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 596 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8990 (m) cc_final: 0.8619 (p) REVERT: A 102 ARG cc_start: 0.6757 (mtt-85) cc_final: 0.6474 (mtt-85) REVERT: A 237 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8047 (mtm-85) REVERT: A 242 LEU cc_start: 0.7964 (mt) cc_final: 0.7561 (mt) REVERT: A 271 GLN cc_start: 0.8307 (mp10) cc_final: 0.7550 (mp10) REVERT: A 278 LYS cc_start: 0.8984 (tttt) cc_final: 0.8714 (ttmt) REVERT: A 298 GLU cc_start: 0.8766 (tp30) cc_final: 0.8434 (tp30) REVERT: A 319 ARG cc_start: 0.8724 (ttp-110) cc_final: 0.8448 (ttm110) REVERT: A 351 TYR cc_start: 0.8707 (p90) cc_final: 0.8347 (p90) REVERT: A 353 TRP cc_start: 0.8416 (p-90) cc_final: 0.8028 (p-90) REVERT: A 398 ASP cc_start: 0.7466 (m-30) cc_final: 0.6759 (m-30) REVERT: A 490 PHE cc_start: 0.8503 (t80) cc_final: 0.8002 (t80) REVERT: A 505 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7694 (m-80) REVERT: A 523 THR cc_start: 0.8610 (p) cc_final: 0.8300 (t) REVERT: A 565 PHE cc_start: 0.7727 (m-80) cc_final: 0.7418 (m-80) REVERT: A 607 GLN cc_start: 0.8582 (mt0) cc_final: 0.8353 (mt0) REVERT: A 725 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: A 804 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8599 (mm-40) REVERT: A 808 ASP cc_start: 0.8059 (t0) cc_final: 0.7749 (t0) REVERT: A 994 ASP cc_start: 0.8622 (t70) cc_final: 0.8326 (t0) REVERT: A 1119 ASN cc_start: 0.8572 (m110) cc_final: 0.8334 (m-40) REVERT: A 1145 LEU cc_start: 0.8777 (mt) cc_final: 0.8297 (mp) REVERT: B 65 PHE cc_start: 0.8788 (m-80) cc_final: 0.8527 (m-80) REVERT: B 99 ASN cc_start: 0.7719 (t0) cc_final: 0.7516 (t0) REVERT: B 108 THR cc_start: 0.7188 (OUTLIER) cc_final: 0.6250 (m) REVERT: B 140 PHE cc_start: 0.8338 (p90) cc_final: 0.8034 (p90) REVERT: B 187 LYS cc_start: 0.7823 (tppt) cc_final: 0.7516 (tptt) REVERT: B 191 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: B 207 HIS cc_start: 0.8253 (t70) cc_final: 0.7482 (t-90) REVERT: B 236 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7852 (p) REVERT: B 281 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8475 (pp20) REVERT: B 298 GLU cc_start: 0.8662 (tt0) cc_final: 0.7968 (tm-30) REVERT: B 319 ARG cc_start: 0.8733 (ttp-110) cc_final: 0.8507 (ttm110) REVERT: B 351 TYR cc_start: 0.8792 (p90) cc_final: 0.8271 (p90) REVERT: B 389 ASP cc_start: 0.7999 (t0) cc_final: 0.7651 (t0) REVERT: B 490 PHE cc_start: 0.8462 (t80) cc_final: 0.8154 (t80) REVERT: B 523 THR cc_start: 0.8556 (p) cc_final: 0.7989 (t) REVERT: B 578 ASP cc_start: 0.8474 (t0) cc_final: 0.8163 (t70) REVERT: B 646 ARG cc_start: 0.9073 (mmm-85) cc_final: 0.8802 (mtt90) REVERT: B 661 GLU cc_start: 0.7784 (pm20) cc_final: 0.7438 (pm20) REVERT: B 776 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8612 (tttt) REVERT: B 796 ASP cc_start: 0.8596 (t0) cc_final: 0.8247 (t0) REVERT: B 808 ASP cc_start: 0.8114 (t0) cc_final: 0.7749 (t0) REVERT: B 823 PHE cc_start: 0.8581 (t80) cc_final: 0.8039 (t80) REVERT: B 902 MET cc_start: 0.8802 (mmm) cc_final: 0.8576 (tpt) REVERT: B 934 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8802 (tt) REVERT: B 994 ASP cc_start: 0.8674 (t70) cc_final: 0.8389 (t0) REVERT: B 1072 GLU cc_start: 0.8607 (pm20) cc_final: 0.8231 (pm20) REVERT: B 1073 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8314 (mttm) REVERT: B 1082 CYS cc_start: 0.7191 (t) cc_final: 0.6889 (t) REVERT: B 1107 ARG cc_start: 0.8432 (mtt90) cc_final: 0.8135 (mpt180) REVERT: B 1123 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.8898 (t) REVERT: C 191 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7500 (mp0) REVERT: C 278 LYS cc_start: 0.8895 (tttt) cc_final: 0.8549 (ttpt) REVERT: C 298 GLU cc_start: 0.8785 (tp30) cc_final: 0.8490 (tp30) REVERT: C 346 ARG cc_start: 0.7670 (tpp80) cc_final: 0.7449 (tpp80) REVERT: C 347 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: C 360 ASN cc_start: 0.8814 (t0) cc_final: 0.8532 (t0) REVERT: C 368 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8883 (pp) REVERT: C 462 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8782 (mmmm) REVERT: C 505 TYR cc_start: 0.7735 (m-80) cc_final: 0.7524 (m-10) REVERT: C 516 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: C 564 GLN cc_start: 0.8505 (tp40) cc_final: 0.8108 (tp40) REVERT: C 578 ASP cc_start: 0.8182 (t0) cc_final: 0.7917 (t70) REVERT: C 643 PHE cc_start: 0.8193 (t80) cc_final: 0.7899 (t80) REVERT: C 710 ASN cc_start: 0.9112 (p0) cc_final: 0.8882 (p0) REVERT: C 776 LYS cc_start: 0.8861 (tttm) cc_final: 0.8485 (tttm) REVERT: C 780 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8148 (mm-30) REVERT: C 787 GLN cc_start: 0.8692 (mt0) cc_final: 0.8264 (mt0) REVERT: C 790 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8751 (mtmt) REVERT: C 794 ILE cc_start: 0.9061 (mm) cc_final: 0.8832 (tp) REVERT: C 796 ASP cc_start: 0.8481 (t0) cc_final: 0.8255 (t0) REVERT: C 814 LYS cc_start: 0.8592 (mmpt) cc_final: 0.8362 (mptt) REVERT: C 994 ASP cc_start: 0.8634 (t70) cc_final: 0.8186 (t0) REVERT: C 1002 GLN cc_start: 0.8697 (tt0) cc_final: 0.8370 (tt0) REVERT: C 1119 ASN cc_start: 0.8853 (m-40) cc_final: 0.8483 (m-40) outliers start: 82 outliers final: 51 residues processed: 644 average time/residue: 0.1868 time to fit residues: 186.3310 Evaluate side-chains 639 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 576 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 38 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 142 optimal weight: 0.6980 chunk 268 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 262 optimal weight: 0.0040 chunk 10 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1005 GLN B 146 HIS B 658 ASN B1005 GLN C 188 ASN C 394 ASN C 969 ASN C1002 GLN C1159 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.110635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.088202 restraints weight = 61128.572| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.57 r_work: 0.3229 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28470 Z= 0.160 Angle : 0.750 15.466 38967 Z= 0.351 Chirality : 0.045 0.280 4716 Planarity : 0.004 0.059 4803 Dihedral : 10.461 111.342 6098 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.24 % Favored : 95.58 % Rotamer: Outliers : 2.96 % Allowed : 15.89 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3300 helix: 2.07 (0.20), residues: 732 sheet: -0.15 (0.19), residues: 714 loop : -1.00 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 102 TYR 0.018 0.001 TYR C1067 PHE 0.022 0.001 PHE B1148 TRP 0.034 0.001 TRP A 104 HIS 0.012 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00355 (28302) covalent geometry : angle 0.71640 (38508) SS BOND : bond 0.00415 ( 45) SS BOND : angle 2.11397 ( 90) hydrogen bonds : bond 0.03782 ( 1092) hydrogen bonds : angle 5.57696 ( 2967) link_ALPHA1-4 : bond 0.01716 ( 27) link_ALPHA1-4 : angle 2.95282 ( 81) link_BETA1-4 : bond 0.00300 ( 36) link_BETA1-4 : angle 1.26044 ( 108) link_BETA1-6 : bond 0.01233 ( 3) link_BETA1-6 : angle 2.27693 ( 9) link_NAG-ASN : bond 0.00348 ( 57) link_NAG-ASN : angle 2.22592 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 583 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6730 (mtt-85) cc_final: 0.6444 (mtt-85) REVERT: A 191 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7530 (mp0) REVERT: A 237 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.8049 (mtm-85) REVERT: A 271 GLN cc_start: 0.8265 (mp10) cc_final: 0.7533 (mp10) REVERT: A 278 LYS cc_start: 0.8996 (tttt) cc_final: 0.8738 (ttmt) REVERT: A 298 GLU cc_start: 0.8748 (tp30) cc_final: 0.8420 (tp30) REVERT: A 319 ARG cc_start: 0.8725 (ttp-110) cc_final: 0.8457 (ttm110) REVERT: A 351 TYR cc_start: 0.8699 (p90) cc_final: 0.8349 (p90) REVERT: A 421 TYR cc_start: 0.7922 (m-80) cc_final: 0.7402 (m-10) REVERT: A 490 PHE cc_start: 0.8518 (t80) cc_final: 0.7992 (t80) REVERT: A 505 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: A 523 THR cc_start: 0.8713 (p) cc_final: 0.8343 (t) REVERT: A 565 PHE cc_start: 0.7717 (m-80) cc_final: 0.7403 (m-80) REVERT: A 607 GLN cc_start: 0.8597 (mt0) cc_final: 0.8390 (mt0) REVERT: A 725 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: A 804 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8612 (mm-40) REVERT: A 808 ASP cc_start: 0.8058 (t0) cc_final: 0.7749 (t0) REVERT: A 994 ASP cc_start: 0.8619 (t70) cc_final: 0.8314 (t0) REVERT: A 1119 ASN cc_start: 0.8581 (m110) cc_final: 0.8359 (m-40) REVERT: B 65 PHE cc_start: 0.8765 (m-80) cc_final: 0.8510 (m-80) REVERT: B 108 THR cc_start: 0.7216 (OUTLIER) cc_final: 0.6319 (m) REVERT: B 140 PHE cc_start: 0.8315 (p90) cc_final: 0.8013 (p90) REVERT: B 191 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: B 207 HIS cc_start: 0.8228 (t70) cc_final: 0.7505 (t-90) REVERT: B 236 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.7880 (p) REVERT: B 281 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8457 (pp20) REVERT: B 287 ASP cc_start: 0.8131 (t0) cc_final: 0.7596 (t0) REVERT: B 298 GLU cc_start: 0.8666 (tt0) cc_final: 0.7981 (tm-30) REVERT: B 306 PHE cc_start: 0.8887 (m-10) cc_final: 0.8491 (m-10) REVERT: B 319 ARG cc_start: 0.8730 (ttp-110) cc_final: 0.8495 (ttm110) REVERT: B 351 TYR cc_start: 0.8745 (p90) cc_final: 0.8276 (p90) REVERT: B 389 ASP cc_start: 0.7984 (t0) cc_final: 0.7641 (t0) REVERT: B 390 LEU cc_start: 0.8805 (tp) cc_final: 0.8596 (tp) REVERT: B 414 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8002 (mm110) REVERT: B 465 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 490 PHE cc_start: 0.8458 (t80) cc_final: 0.8156 (t80) REVERT: B 523 THR cc_start: 0.8564 (p) cc_final: 0.7992 (t) REVERT: B 534 VAL cc_start: 0.9124 (p) cc_final: 0.8899 (m) REVERT: B 578 ASP cc_start: 0.8470 (t0) cc_final: 0.8152 (t70) REVERT: B 646 ARG cc_start: 0.9087 (mmm-85) cc_final: 0.8827 (mtt90) REVERT: B 661 GLU cc_start: 0.7802 (pm20) cc_final: 0.7468 (pm20) REVERT: B 776 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8628 (tttt) REVERT: B 796 ASP cc_start: 0.8567 (t0) cc_final: 0.8228 (t0) REVERT: B 808 ASP cc_start: 0.8064 (t0) cc_final: 0.7725 (t0) REVERT: B 823 PHE cc_start: 0.8558 (t80) cc_final: 0.8046 (t80) REVERT: B 934 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8792 (tt) REVERT: B 994 ASP cc_start: 0.8557 (t70) cc_final: 0.8250 (t0) REVERT: B 1072 GLU cc_start: 0.8580 (pm20) cc_final: 0.8220 (pm20) REVERT: B 1073 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8346 (mttm) REVERT: B 1082 CYS cc_start: 0.7167 (t) cc_final: 0.6855 (t) REVERT: B 1123 SER cc_start: 0.9290 (OUTLIER) cc_final: 0.8931 (t) REVERT: C 191 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7814 (mp0) REVERT: C 278 LYS cc_start: 0.8905 (tttt) cc_final: 0.8571 (ttpt) REVERT: C 298 GLU cc_start: 0.8781 (tp30) cc_final: 0.8477 (tp30) REVERT: C 347 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.6774 (m-80) REVERT: C 360 ASN cc_start: 0.8813 (t0) cc_final: 0.8607 (t0) REVERT: C 368 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8899 (pp) REVERT: C 462 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8796 (mmmm) REVERT: C 564 GLN cc_start: 0.8465 (tp40) cc_final: 0.8114 (tp40) REVERT: C 578 ASP cc_start: 0.8179 (t0) cc_final: 0.7786 (t70) REVERT: C 643 PHE cc_start: 0.8174 (t80) cc_final: 0.7861 (t80) REVERT: C 710 ASN cc_start: 0.9108 (p0) cc_final: 0.8887 (p0) REVERT: C 776 LYS cc_start: 0.8880 (tttm) cc_final: 0.8490 (ttpp) REVERT: C 780 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8129 (mm-30) REVERT: C 787 GLN cc_start: 0.8679 (mt0) cc_final: 0.8280 (mt0) REVERT: C 796 ASP cc_start: 0.8450 (t0) cc_final: 0.8238 (t0) REVERT: C 814 LYS cc_start: 0.8593 (mmpt) cc_final: 0.8367 (mptt) REVERT: C 817 PHE cc_start: 0.8216 (t80) cc_final: 0.7990 (t80) REVERT: C 994 ASP cc_start: 0.8640 (t70) cc_final: 0.8194 (t0) REVERT: C 1092 GLU cc_start: 0.8226 (pm20) cc_final: 0.7862 (pm20) REVERT: C 1119 ASN cc_start: 0.8838 (m-40) cc_final: 0.8489 (m-40) outliers start: 86 outliers final: 57 residues processed: 636 average time/residue: 0.1844 time to fit residues: 182.4612 Evaluate side-chains 635 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 568 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 218 optimal weight: 0.9990 chunk 29 optimal weight: 0.0050 chunk 212 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 198 optimal weight: 0.5980 chunk 313 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 242 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 804 GLN A 954 GLN B 146 HIS B1005 GLN C 188 ASN C 394 ASN C 969 ASN C1002 GLN C1159 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.111202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088994 restraints weight = 60652.955| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.54 r_work: 0.3233 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28470 Z= 0.147 Angle : 0.752 16.315 38967 Z= 0.351 Chirality : 0.045 0.278 4716 Planarity : 0.004 0.053 4803 Dihedral : 9.983 110.579 6098 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.27 % Favored : 95.55 % Rotamer: Outliers : 2.76 % Allowed : 16.48 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3300 helix: 2.12 (0.20), residues: 732 sheet: -0.10 (0.19), residues: 690 loop : -0.96 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 102 TYR 0.019 0.001 TYR C1067 PHE 0.022 0.001 PHE C 817 TRP 0.036 0.001 TRP A 104 HIS 0.013 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00323 (28302) covalent geometry : angle 0.71892 (38508) SS BOND : bond 0.00439 ( 45) SS BOND : angle 2.01547 ( 90) hydrogen bonds : bond 0.03670 ( 1092) hydrogen bonds : angle 5.57754 ( 2967) link_ALPHA1-4 : bond 0.01693 ( 27) link_ALPHA1-4 : angle 3.01282 ( 81) link_BETA1-4 : bond 0.00327 ( 36) link_BETA1-4 : angle 1.23704 ( 108) link_BETA1-6 : bond 0.01308 ( 3) link_BETA1-6 : angle 2.39097 ( 9) link_NAG-ASN : bond 0.00347 ( 57) link_NAG-ASN : angle 2.19200 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 576 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6742 (mtt-85) cc_final: 0.6452 (mtt-85) REVERT: A 158 ARG cc_start: 0.7078 (mmt-90) cc_final: 0.6771 (mmt-90) REVERT: A 191 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7451 (mp0) REVERT: A 220 PHE cc_start: 0.8199 (t80) cc_final: 0.7922 (t80) REVERT: A 237 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8057 (mtm-85) REVERT: A 271 GLN cc_start: 0.8265 (mp10) cc_final: 0.7526 (mp10) REVERT: A 278 LYS cc_start: 0.8989 (tttt) cc_final: 0.8728 (ttmt) REVERT: A 298 GLU cc_start: 0.8758 (tp30) cc_final: 0.8426 (tp30) REVERT: A 319 ARG cc_start: 0.8713 (ttp-110) cc_final: 0.8444 (ttm110) REVERT: A 351 TYR cc_start: 0.8691 (p90) cc_final: 0.8333 (p90) REVERT: A 421 TYR cc_start: 0.7858 (m-80) cc_final: 0.7316 (m-10) REVERT: A 490 PHE cc_start: 0.8511 (t80) cc_final: 0.7989 (t80) REVERT: A 505 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: A 523 THR cc_start: 0.8741 (p) cc_final: 0.8398 (t) REVERT: A 565 PHE cc_start: 0.7781 (m-80) cc_final: 0.7449 (m-80) REVERT: A 725 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: A 790 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8560 (mtmt) REVERT: A 808 ASP cc_start: 0.8083 (t0) cc_final: 0.7801 (t0) REVERT: A 817 PHE cc_start: 0.8425 (t80) cc_final: 0.8170 (t80) REVERT: A 994 ASP cc_start: 0.8614 (t70) cc_final: 0.8303 (t0) REVERT: A 1119 ASN cc_start: 0.8567 (m110) cc_final: 0.8335 (m-40) REVERT: B 65 PHE cc_start: 0.8765 (m-80) cc_final: 0.8519 (m-80) REVERT: B 108 THR cc_start: 0.7165 (OUTLIER) cc_final: 0.6207 (m) REVERT: B 140 PHE cc_start: 0.8332 (p90) cc_final: 0.8006 (p90) REVERT: B 191 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: B 207 HIS cc_start: 0.8287 (t70) cc_final: 0.7467 (t-90) REVERT: B 236 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.7865 (p) REVERT: B 281 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8481 (pp20) REVERT: B 287 ASP cc_start: 0.8260 (t0) cc_final: 0.7749 (t0) REVERT: B 298 GLU cc_start: 0.8667 (tt0) cc_final: 0.7970 (tm-30) REVERT: B 306 PHE cc_start: 0.8874 (m-10) cc_final: 0.8609 (m-10) REVERT: B 319 ARG cc_start: 0.8725 (ttp-110) cc_final: 0.8452 (ttm110) REVERT: B 351 TYR cc_start: 0.8730 (p90) cc_final: 0.8241 (p90) REVERT: B 389 ASP cc_start: 0.7931 (t0) cc_final: 0.7583 (t0) REVERT: B 390 LEU cc_start: 0.8791 (tp) cc_final: 0.8585 (tp) REVERT: B 403 ARG cc_start: 0.7730 (ttp-110) cc_final: 0.7402 (mtm110) REVERT: B 414 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8027 (mm110) REVERT: B 465 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7608 (mt-10) REVERT: B 490 PHE cc_start: 0.8439 (t80) cc_final: 0.8150 (t80) REVERT: B 523 THR cc_start: 0.8581 (p) cc_final: 0.8020 (t) REVERT: B 534 VAL cc_start: 0.9131 (p) cc_final: 0.8909 (m) REVERT: B 578 ASP cc_start: 0.8510 (t0) cc_final: 0.8188 (t70) REVERT: B 646 ARG cc_start: 0.9044 (mmm-85) cc_final: 0.8771 (mtt90) REVERT: B 661 GLU cc_start: 0.7771 (pm20) cc_final: 0.7462 (pm20) REVERT: B 776 LYS cc_start: 0.8899 (ttmm) cc_final: 0.8629 (tttt) REVERT: B 796 ASP cc_start: 0.8564 (t0) cc_final: 0.8227 (t0) REVERT: B 808 ASP cc_start: 0.8026 (t0) cc_final: 0.7682 (t0) REVERT: B 817 PHE cc_start: 0.8573 (t80) cc_final: 0.7926 (t80) REVERT: B 823 PHE cc_start: 0.8537 (t80) cc_final: 0.8018 (t80) REVERT: B 986 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8203 (mmmt) REVERT: B 990 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7635 (mp0) REVERT: B 994 ASP cc_start: 0.8549 (t70) cc_final: 0.8240 (t0) REVERT: B 1072 GLU cc_start: 0.8571 (pm20) cc_final: 0.8279 (pm20) REVERT: B 1073 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8338 (mttm) REVERT: B 1082 CYS cc_start: 0.7155 (t) cc_final: 0.6836 (t) REVERT: B 1123 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.9057 (t) REVERT: C 191 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7824 (mp0) REVERT: C 278 LYS cc_start: 0.8898 (tttt) cc_final: 0.8567 (ttpt) REVERT: C 296 LEU cc_start: 0.8894 (tp) cc_final: 0.8569 (tt) REVERT: C 298 GLU cc_start: 0.8776 (tp30) cc_final: 0.8467 (tp30) REVERT: C 347 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6802 (m-80) REVERT: C 360 ASN cc_start: 0.8810 (t0) cc_final: 0.8560 (t0) REVERT: C 368 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8884 (pp) REVERT: C 564 GLN cc_start: 0.8469 (tp40) cc_final: 0.8090 (tp40) REVERT: C 578 ASP cc_start: 0.8115 (t0) cc_final: 0.7910 (t70) REVERT: C 643 PHE cc_start: 0.8146 (t80) cc_final: 0.7837 (t80) REVERT: C 702 GLU cc_start: 0.8394 (tp30) cc_final: 0.8091 (tp30) REVERT: C 710 ASN cc_start: 0.9093 (p0) cc_final: 0.8867 (p0) REVERT: C 776 LYS cc_start: 0.8866 (tttm) cc_final: 0.8472 (ttpp) REVERT: C 780 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 787 GLN cc_start: 0.8673 (mt0) cc_final: 0.8264 (mt0) REVERT: C 796 ASP cc_start: 0.8480 (t0) cc_final: 0.8260 (t0) REVERT: C 814 LYS cc_start: 0.8597 (mmpt) cc_final: 0.8373 (mptt) REVERT: C 994 ASP cc_start: 0.8645 (t70) cc_final: 0.8206 (t0) REVERT: C 1002 GLN cc_start: 0.8657 (tt0) cc_final: 0.8312 (tt0) REVERT: C 1092 GLU cc_start: 0.8189 (pm20) cc_final: 0.7827 (pm20) REVERT: C 1119 ASN cc_start: 0.8811 (m-40) cc_final: 0.8491 (m-40) outliers start: 80 outliers final: 54 residues processed: 630 average time/residue: 0.1836 time to fit residues: 180.3524 Evaluate side-chains 626 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 563 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 212 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 315 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 197 optimal weight: 0.2980 chunk 264 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 330 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 30 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 804 GLN B1005 GLN C 394 ASN C 969 ASN C1159 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.111393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089133 restraints weight = 60939.321| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.56 r_work: 0.3234 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28470 Z= 0.151 Angle : 0.752 14.926 38967 Z= 0.353 Chirality : 0.045 0.279 4716 Planarity : 0.004 0.058 4803 Dihedral : 9.804 110.426 6098 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.21 % Favored : 95.61 % Rotamer: Outliers : 2.52 % Allowed : 17.06 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3300 helix: 2.13 (0.20), residues: 732 sheet: -0.19 (0.18), residues: 714 loop : -0.95 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 102 TYR 0.031 0.001 TYR C 904 PHE 0.023 0.001 PHE C 855 TRP 0.034 0.002 TRP A 104 HIS 0.012 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00333 (28302) covalent geometry : angle 0.71952 (38508) SS BOND : bond 0.00431 ( 45) SS BOND : angle 1.97724 ( 90) hydrogen bonds : bond 0.03658 ( 1092) hydrogen bonds : angle 5.57545 ( 2967) link_ALPHA1-4 : bond 0.01688 ( 27) link_ALPHA1-4 : angle 2.99913 ( 81) link_BETA1-4 : bond 0.00315 ( 36) link_BETA1-4 : angle 1.23298 ( 108) link_BETA1-6 : bond 0.01338 ( 3) link_BETA1-6 : angle 2.45424 ( 9) link_NAG-ASN : bond 0.00343 ( 57) link_NAG-ASN : angle 2.17961 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 570 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6749 (mtt-85) cc_final: 0.6452 (mtt-85) REVERT: A 153 MET cc_start: 0.7104 (mpp) cc_final: 0.6800 (mpp) REVERT: A 158 ARG cc_start: 0.7098 (mmt-90) cc_final: 0.6878 (mmt-90) REVERT: A 191 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7447 (mp0) REVERT: A 220 PHE cc_start: 0.8192 (t80) cc_final: 0.7874 (t80) REVERT: A 269 TYR cc_start: 0.7334 (m-10) cc_final: 0.6901 (m-80) REVERT: A 271 GLN cc_start: 0.8276 (mp10) cc_final: 0.7539 (mp10) REVERT: A 278 LYS cc_start: 0.8997 (tttt) cc_final: 0.8739 (ttmt) REVERT: A 298 GLU cc_start: 0.8757 (tp30) cc_final: 0.8423 (tp30) REVERT: A 319 ARG cc_start: 0.8713 (ttp-110) cc_final: 0.8446 (ttm110) REVERT: A 351 TYR cc_start: 0.8698 (p90) cc_final: 0.8327 (p90) REVERT: A 353 TRP cc_start: 0.8408 (p-90) cc_final: 0.8081 (p-90) REVERT: A 421 TYR cc_start: 0.7873 (m-80) cc_final: 0.7319 (m-10) REVERT: A 490 PHE cc_start: 0.8510 (t80) cc_final: 0.7980 (t80) REVERT: A 505 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7696 (m-80) REVERT: A 523 THR cc_start: 0.8769 (p) cc_final: 0.8430 (t) REVERT: A 562 PHE cc_start: 0.8177 (p90) cc_final: 0.7933 (p90) REVERT: A 565 PHE cc_start: 0.7776 (m-80) cc_final: 0.7442 (m-80) REVERT: A 725 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: A 790 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8564 (mtmt) REVERT: A 808 ASP cc_start: 0.8077 (t0) cc_final: 0.7807 (t0) REVERT: A 994 ASP cc_start: 0.8615 (t70) cc_final: 0.8302 (t0) REVERT: A 1119 ASN cc_start: 0.8586 (m110) cc_final: 0.8360 (m-40) REVERT: B 65 PHE cc_start: 0.8762 (m-80) cc_final: 0.8523 (m-80) REVERT: B 108 THR cc_start: 0.7195 (OUTLIER) cc_final: 0.6245 (m) REVERT: B 140 PHE cc_start: 0.8324 (p90) cc_final: 0.8005 (p90) REVERT: B 191 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: B 207 HIS cc_start: 0.8302 (t70) cc_final: 0.7418 (t-90) REVERT: B 236 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7867 (p) REVERT: B 281 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8453 (pp20) REVERT: B 287 ASP cc_start: 0.8293 (t0) cc_final: 0.7794 (t0) REVERT: B 298 GLU cc_start: 0.8678 (tt0) cc_final: 0.8005 (tm-30) REVERT: B 306 PHE cc_start: 0.8878 (m-10) cc_final: 0.8584 (m-10) REVERT: B 319 ARG cc_start: 0.8723 (ttp-110) cc_final: 0.8449 (ttm110) REVERT: B 351 TYR cc_start: 0.8701 (p90) cc_final: 0.8237 (p90) REVERT: B 389 ASP cc_start: 0.7933 (t0) cc_final: 0.7583 (t0) REVERT: B 390 LEU cc_start: 0.8776 (tp) cc_final: 0.8574 (tp) REVERT: B 403 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7429 (mtm110) REVERT: B 414 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8032 (mm110) REVERT: B 465 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7533 (mt-10) REVERT: B 490 PHE cc_start: 0.8450 (t80) cc_final: 0.8152 (t80) REVERT: B 523 THR cc_start: 0.8582 (p) cc_final: 0.8011 (t) REVERT: B 578 ASP cc_start: 0.8506 (t0) cc_final: 0.8184 (t70) REVERT: B 646 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8798 (mtt90) REVERT: B 661 GLU cc_start: 0.7781 (pm20) cc_final: 0.7464 (pm20) REVERT: B 776 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8622 (tttt) REVERT: B 796 ASP cc_start: 0.8567 (t0) cc_final: 0.8229 (t0) REVERT: B 808 ASP cc_start: 0.8037 (t0) cc_final: 0.7729 (t0) REVERT: B 817 PHE cc_start: 0.8589 (t80) cc_final: 0.7941 (t80) REVERT: B 823 PHE cc_start: 0.8532 (t80) cc_final: 0.8009 (t80) REVERT: B 986 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8199 (mmmt) REVERT: B 990 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7624 (mp0) REVERT: B 994 ASP cc_start: 0.8558 (t70) cc_final: 0.8250 (t0) REVERT: B 1072 GLU cc_start: 0.8553 (pm20) cc_final: 0.8286 (pm20) REVERT: B 1073 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8345 (mttm) REVERT: B 1082 CYS cc_start: 0.7176 (t) cc_final: 0.6854 (t) REVERT: B 1123 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.9062 (t) REVERT: C 191 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7792 (mp0) REVERT: C 278 LYS cc_start: 0.8913 (tttt) cc_final: 0.8587 (ttpt) REVERT: C 296 LEU cc_start: 0.8902 (tp) cc_final: 0.8573 (tt) REVERT: C 298 GLU cc_start: 0.8779 (tp30) cc_final: 0.8475 (tp30) REVERT: C 347 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6811 (m-80) REVERT: C 360 ASN cc_start: 0.8817 (t0) cc_final: 0.8606 (t0) REVERT: C 368 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8892 (pp) REVERT: C 563 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8290 (mm-40) REVERT: C 564 GLN cc_start: 0.8466 (tp40) cc_final: 0.8104 (tp40) REVERT: C 578 ASP cc_start: 0.8129 (t0) cc_final: 0.7835 (t70) REVERT: C 643 PHE cc_start: 0.8158 (t80) cc_final: 0.7839 (t80) REVERT: C 702 GLU cc_start: 0.8422 (tp30) cc_final: 0.8110 (tp30) REVERT: C 710 ASN cc_start: 0.9090 (p0) cc_final: 0.8864 (p0) REVERT: C 776 LYS cc_start: 0.8871 (tttm) cc_final: 0.8478 (ttpp) REVERT: C 780 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8124 (mm-30) REVERT: C 787 GLN cc_start: 0.8670 (mt0) cc_final: 0.8274 (mt0) REVERT: C 796 ASP cc_start: 0.8483 (t0) cc_final: 0.8262 (t0) REVERT: C 814 LYS cc_start: 0.8606 (mmpt) cc_final: 0.8395 (mptt) REVERT: C 994 ASP cc_start: 0.8641 (t70) cc_final: 0.8193 (t0) REVERT: C 1002 GLN cc_start: 0.8659 (tt0) cc_final: 0.8312 (tt0) REVERT: C 1092 GLU cc_start: 0.8194 (pm20) cc_final: 0.7833 (pm20) REVERT: C 1119 ASN cc_start: 0.8805 (m-40) cc_final: 0.8492 (m-40) outliers start: 73 outliers final: 59 residues processed: 618 average time/residue: 0.1889 time to fit residues: 180.4876 Evaluate side-chains 629 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 561 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 157 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 279 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 283 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 804 GLN B1005 GLN C 394 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN C1159 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.111348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.089202 restraints weight = 60810.597| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.54 r_work: 0.3241 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.005 0.220 28470 Z= 0.204 Angle : 0.936 59.174 38967 Z= 0.501 Chirality : 0.047 0.819 4716 Planarity : 0.004 0.058 4803 Dihedral : 9.791 110.427 6094 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.30 % Favored : 95.52 % Rotamer: Outliers : 2.48 % Allowed : 17.24 % Favored : 80.28 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3300 helix: 2.13 (0.19), residues: 732 sheet: -0.21 (0.18), residues: 714 loop : -0.95 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 102 TYR 0.039 0.001 TYR B 380 PHE 0.023 0.001 PHE C 855 TRP 0.029 0.002 TRP A 104 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00460 (28302) covalent geometry : angle 0.90952 (38508) SS BOND : bond 0.00400 ( 45) SS BOND : angle 2.39117 ( 90) hydrogen bonds : bond 0.03668 ( 1092) hydrogen bonds : angle 5.57861 ( 2967) link_ALPHA1-4 : bond 0.01704 ( 27) link_ALPHA1-4 : angle 3.00362 ( 81) link_BETA1-4 : bond 0.00312 ( 36) link_BETA1-4 : angle 1.23610 ( 108) link_BETA1-6 : bond 0.01333 ( 3) link_BETA1-6 : angle 2.45361 ( 9) link_NAG-ASN : bond 0.00344 ( 57) link_NAG-ASN : angle 2.18035 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7153.94 seconds wall clock time: 123 minutes 9.40 seconds (7389.40 seconds total)