Starting phenix.real_space_refine on Sun Jun 22 08:16:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tei_25846/06_2025/7tei_25846.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tei_25846/06_2025/7tei_25846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tei_25846/06_2025/7tei_25846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tei_25846/06_2025/7tei_25846.map" model { file = "/net/cci-nas-00/data/ceres_data/7tei_25846/06_2025/7tei_25846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tei_25846/06_2025/7tei_25846.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.168 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 105 5.16 5 C 16177 2.51 5 N 4045 2.21 5 O 5093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25420 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 7993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7993 Classifications: {'peptide': 1019} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 968} Chain breaks: 8 Chain: "B" Number of atoms: 8179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8179 Classifications: {'peptide': 1042} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 991} Chain breaks: 6 Chain: "C" Number of atoms: 7729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7729 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 48, 'TRANS': 934} Chain breaks: 9 Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "3" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "1A" 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: "3A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "kA" 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: "mA" 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: "NA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "oA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "QA" 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: "rA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "SA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "wA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "YA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 15.05, per 1000 atoms: 0.59 Number of scatterers: 25420 At special positions: 0 Unit cell: (131.76, 137.16, 201.96, 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 105 16.00 O 5093 8.00 N 4045 7.00 C 16177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA 7 3 " - " MAN 7 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA v 3 " - " MAN v 4 " " BMAYA 3 " - " MANYA 4 " " BMArA 3 " - " MANrA 4 " " BMAwA 3 " - " MANwA 4 " ALPHA1-6 " BMA 7 3 " - " MAN 7 5 " " BMA P 3 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 5 " " BMA v 3 " - " MAN v 5 " " BMAYA 3 " - " MANYA 5 " " BMArA 3 " - " MANrA 5 " " BMAwA 3 " - " MANwA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " 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 G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG j 1 " - " NAG j 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG1A 1 " - " NAG1A 2 " " NAG3A 1 " - " NAG3A 2 " " NAG3A 2 " - " BMA3A 3 " " NAGNA 1 " - " NAGNA 2 " " NAGNA 2 " - " BMANA 3 " " NAGQA 1 " - " NAGQA 2 " " NAGSA 1 " - " NAGSA 2 " " NAGSA 2 " - " BMASA 3 " " NAGYA 1 " - " NAGYA 2 " " NAGYA 2 " - " BMAYA 3 " " NAGkA 1 " - " NAGkA 2 " " NAGmA 1 " - " NAGmA 2 " " NAGoA 1 " - " NAGoA 2 " " NAGoA 2 " - " BMAoA 3 " " NAGrA 1 " - " NAGrA 2 " " NAGrA 2 " - " BMArA 3 " " NAGwA 1 " - " NAGwA 2 " " NAGwA 2 " - " BMAwA 3 " NAG-ASN " NAG 0 1 " - " ASN A 801 " " NAG 3 1 " - " ASN A1074 " " NAG 7 1 " - " ASN A1134 " " NAG A1201 " - " ASN A 331 " " NAG A1202 " - " ASN A 343 " " NAG A1203 " - " ASN A1098 " " NAG A1204 " - " ASN A 234 " " NAG A1205 " - " ASN A 657 " " NAG A1206 " - " ASN A 709 " " NAG A1207 " - " ASN A 122 " " NAG A1208 " - " ASN A 61 " " NAG B1201 " - " ASN B 343 " " NAG B1202 " - " ASN B 616 " " NAG B1203 " - " ASN B1134 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 616 " " NAG C1203 " - " ASN C1098 " " NAG C1204 " - " ASN C 234 " " NAG D 1 " - " ASN A 282 " " NAG E 1 " - " ASN A 616 " " NAG F 1 " - " ASN B 234 " " NAG G 1 " - " ASN B 331 " " NAG H 1 " - " ASN C 282 " " NAG I 1 " - " ASN C 122 " " NAG J 1 " - " ASN C 165 " " NAG K 1 " - " ASN C 331 " " NAG L 1 " - " ASN C 343 " " NAG M 1 " - " ASN C 603 " " NAG N 1 " - " ASN C 657 " " NAG O 1 " - " ASN C 709 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1074 " " NAG S 1 " - " ASN C1134 " " NAG W 1 " - " ASN A 165 " " NAG j 1 " - " ASN A 603 " " NAG v 1 " - " ASN A 717 " " NAG1A 1 " - " ASN B1074 " " NAG3A 1 " - " ASN B1098 " " NAGNA 1 " - " ASN B 61 " " NAGQA 1 " - " ASN B 122 " " NAGSA 1 " - " ASN B 165 " " NAGYA 1 " - " ASN B 282 " " NAGkA 1 " - " ASN B 603 " " NAGmA 1 " - " ASN B 657 " " NAGoA 1 " - " ASN B 709 " " NAGrA 1 " - " ASN B 717 " " NAGwA 1 " - " ASN B 801 " Time building additional restraints: 7.30 Conformation dependent library (CDL) restraints added in 3.0 seconds 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5726 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 42 sheets defined 25.5% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.180A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.068A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 removed outlier: 3.596A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 757 removed outlier: 3.730A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.638A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 849 through 855 removed outlier: 3.607A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.815A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.516A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.280A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.661A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 3.832A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.744A 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) removed outlier: 3.638A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.065A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 737 through 743 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: 3.528A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.714A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.634A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.015A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.541A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.157A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.532A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.284A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.862A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 336 through 341 removed outlier: 4.513A pdb=" N ASP C 339 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.588A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.645A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.570A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.664A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.867A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.540A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.106A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 958 " --> pdb=" O HIS C 954 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (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: 3.570A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.765A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.051A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.183A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.554A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.897A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.629A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.606A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.763A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.239A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.675A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.501A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.688A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.703A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.969A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.713A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.315A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.068A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.040A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.872A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 315 removed outlier: 3.888A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.554A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 356 through 359 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.044A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.656A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.972A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.658A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.522A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 30 removed outlier: 8.002A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.626A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.703A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.913A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.600A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.016A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.920A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.943A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.582A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.529A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 963 hydrogen bonds defined for protein. 2655 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: 10.37 Time building geometry restraints manager: 8.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7800 1.35 - 1.47: 6680 1.47 - 1.59: 11354 1.59 - 1.71: 4 1.71 - 1.83: 129 Bond restraints: 25967 Sorted by residual: bond pdb=" C1 BMA W 3 " pdb=" C2 BMA W 3 " ideal model delta sigma weight residual 1.519 1.620 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C1 BMA 0 3 " pdb=" C2 BMA 0 3 " ideal model delta sigma weight residual 1.519 1.619 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C1 BMA L 3 " pdb=" C2 BMA L 3 " ideal model delta sigma weight residual 1.519 1.611 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 NAGmA 2 " pdb=" O5 NAGmA 2 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 25962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 34800 2.79 - 5.57: 428 5.57 - 8.36: 72 8.36 - 11.14: 8 11.14 - 13.93: 2 Bond angle restraints: 35310 Sorted by residual: angle pdb=" C ASN B 87 " pdb=" N ASP B 88 " pdb=" CA ASP B 88 " ideal model delta sigma weight residual 122.46 128.60 -6.14 1.41e+00 5.03e-01 1.89e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.46 128.48 -6.02 1.41e+00 5.03e-01 1.82e+01 angle pdb=" CB GLN B1142 " pdb=" CG GLN B1142 " pdb=" CD GLN B1142 " ideal model delta sigma weight residual 112.60 119.65 -7.05 1.70e+00 3.46e-01 1.72e+01 angle pdb=" C PHE C 32 " pdb=" N THR C 33 " pdb=" CA THR C 33 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" CB GLN A1142 " pdb=" CG GLN A1142 " pdb=" CD GLN A1142 " ideal model delta sigma weight residual 112.60 119.02 -6.42 1.70e+00 3.46e-01 1.43e+01 ... (remaining 35305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 15669 21.90 - 43.79: 906 43.79 - 65.69: 160 65.69 - 87.59: 143 87.59 - 109.48: 79 Dihedral angle restraints: 16957 sinusoidal: 8075 harmonic: 8882 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.57 78.57 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual -86.00 -158.58 72.58 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.93 67.93 1 1.00e+01 1.00e-02 5.99e+01 ... (remaining 16954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3896 0.095 - 0.191: 427 0.191 - 0.286: 28 0.286 - 0.382: 13 0.382 - 0.477: 1 Chirality restraints: 4365 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" C1 NAG C1203 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1203 " pdb=" O5 NAG C1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" C5 BMArA 3 " pdb=" C4 BMArA 3 " pdb=" C6 BMArA 3 " pdb=" O5 BMArA 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.65 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 4362 not shown) Planarity restraints: 4417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO C 463 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 208 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO B 209 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO A 295 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.030 5.00e-02 4.00e+02 ... (remaining 4414 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 6022 2.79 - 3.32: 20894 3.32 - 3.85: 40973 3.85 - 4.37: 46663 4.37 - 4.90: 82816 Nonbonded interactions: 197368 Sorted by model distance: nonbonded pdb=" O LEU B 293 " pdb=" OG1 THR B 632 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.299 3.040 nonbonded pdb=" OE1 GLN B 965 " pdb=" OG SER B1003 " model vdw 2.303 3.040 nonbonded pdb=" O VAL B 401 " pdb=" OH TYR B 453 " model vdw 2.306 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.311 3.040 ... (remaining 197363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '3' selection = chain '3A' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'NA' selection = chain 'SA' selection = chain 'W' selection = chain 'oA' } ncs_group { reference = chain '1A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'QA' selection = chain 'R' selection = chain 'j' selection = chain 'kA' selection = chain 'mA' } ncs_group { reference = chain '7' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'YA' selection = chain 'rA' selection = chain 'v' selection = chain 'wA' } ncs_group { reference = (chain 'A' and (resid 27 through 474 or resid 489 through 519 or resid 527 throu \ gh 621 or resid 640 through 675 or resid 689 through 827 or resid 854 through 11 \ 47 or resid 1201 through 1203)) selection = (chain 'B' and (resid 27 through 210 or resid 215 through 474 or resid 489 throu \ gh 621 or resid 640 through 675 or resid 689 through 827 or resid 854 through 11 \ 47 or resid 1201 through 1203)) selection = (chain 'C' and (resid 27 through 519 or resid 527 through 1147 or resid 1201 thr \ ough 1203)) } 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: 2.270 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: 0.990 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 58.870 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.200 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.006 0.101 26121 Z= 0.279 Angle : 0.926 23.235 35734 Z= 0.408 Chirality : 0.059 0.477 4365 Planarity : 0.006 0.057 4369 Dihedral : 17.702 109.485 11117 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 2992 helix: -0.89 (0.17), residues: 686 sheet: 0.56 (0.19), residues: 681 loop : -1.07 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.004 0.001 HIS B1048 PHE 0.032 0.002 PHE A 906 TYR 0.031 0.002 TYR B 904 ARG 0.006 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 48) link_NAG-ASN : angle 3.06901 ( 144) link_ALPHA1-6 : bond 0.00659 ( 8) link_ALPHA1-6 : angle 1.59948 ( 24) link_BETA1-4 : bond 0.02300 ( 52) link_BETA1-4 : angle 6.63300 ( 156) link_ALPHA1-3 : bond 0.00811 ( 8) link_ALPHA1-3 : angle 1.59810 ( 24) hydrogen bonds : bond 0.13790 ( 961) hydrogen bonds : angle 7.07531 ( 2655) SS BOND : bond 0.00315 ( 38) SS BOND : angle 1.03750 ( 76) covalent geometry : bond 0.00565 (25967) covalent geometry : angle 0.79306 (35310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 2.951 Fit side-chains REVERT: C 460 ASN cc_start: 0.7497 (m-40) cc_final: 0.6879 (m110) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3541 time to fit residues: 38.6580 Evaluate side-chains 48 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 127 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 237 optimal weight: 30.0000 chunk 91 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 275 optimal weight: 0.0970 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1106 GLN B 188 ASN B 625 HIS B1054 GLN C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.099224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.071067 restraints weight = 66444.819| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.90 r_work: 0.2904 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26121 Z= 0.141 Angle : 0.670 18.672 35734 Z= 0.293 Chirality : 0.048 0.382 4365 Planarity : 0.004 0.046 4369 Dihedral : 13.949 85.974 5628 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.22 % Allowed : 2.88 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 2992 helix: 0.80 (0.20), residues: 683 sheet: 0.59 (0.19), residues: 678 loop : -0.89 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 353 HIS 0.005 0.001 HIS B 207 PHE 0.025 0.001 PHE A 374 TYR 0.017 0.001 TYR C1067 ARG 0.005 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 48) link_NAG-ASN : angle 2.30470 ( 144) link_ALPHA1-6 : bond 0.00615 ( 8) link_ALPHA1-6 : angle 2.06386 ( 24) link_BETA1-4 : bond 0.01617 ( 52) link_BETA1-4 : angle 4.70632 ( 156) link_ALPHA1-3 : bond 0.01136 ( 8) link_ALPHA1-3 : angle 3.10114 ( 24) hydrogen bonds : bond 0.03937 ( 961) hydrogen bonds : angle 5.29884 ( 2655) SS BOND : bond 0.00277 ( 38) SS BOND : angle 0.74021 ( 76) covalent geometry : bond 0.00306 (25967) covalent geometry : angle 0.56889 (35310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 2.704 Fit side-chains REVERT: C 460 ASN cc_start: 0.8136 (m-40) cc_final: 0.7664 (m110) REVERT: C 904 TYR cc_start: 0.8278 (m-10) cc_final: 0.7985 (m-10) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.3604 time to fit residues: 34.8905 Evaluate side-chains 49 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 365 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 164 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 chunk 270 optimal weight: 0.9980 chunk 260 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.098714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.070285 restraints weight = 66183.049| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.11 r_work: 0.2888 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26121 Z= 0.143 Angle : 0.644 18.825 35734 Z= 0.281 Chirality : 0.048 0.368 4365 Planarity : 0.003 0.040 4369 Dihedral : 10.977 77.121 5628 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.26 % Allowed : 4.65 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 2992 helix: 1.34 (0.21), residues: 684 sheet: 0.51 (0.19), residues: 675 loop : -0.80 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.004 0.001 HIS B 207 PHE 0.020 0.001 PHE A 374 TYR 0.025 0.001 TYR B 837 ARG 0.002 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 48) link_NAG-ASN : angle 2.18499 ( 144) link_ALPHA1-6 : bond 0.00775 ( 8) link_ALPHA1-6 : angle 2.03057 ( 24) link_BETA1-4 : bond 0.01711 ( 52) link_BETA1-4 : angle 4.60126 ( 156) link_ALPHA1-3 : bond 0.01454 ( 8) link_ALPHA1-3 : angle 2.05215 ( 24) hydrogen bonds : bond 0.03888 ( 961) hydrogen bonds : angle 4.98633 ( 2655) SS BOND : bond 0.00283 ( 38) SS BOND : angle 0.72301 ( 76) covalent geometry : bond 0.00315 (25967) covalent geometry : angle 0.54761 (35310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 2.784 Fit side-chains REVERT: C 460 ASN cc_start: 0.8248 (m-40) cc_final: 0.7904 (m110) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.3373 time to fit residues: 35.1108 Evaluate side-chains 49 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 994 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 232 optimal weight: 20.0000 chunk 72 optimal weight: 0.0270 chunk 49 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 160 optimal weight: 0.0870 overall best weight: 2.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 580 GLN B 188 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.097982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063638 restraints weight = 66969.320| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.43 r_work: 0.2904 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26121 Z= 0.160 Angle : 0.640 18.498 35734 Z= 0.282 Chirality : 0.048 0.366 4365 Planarity : 0.003 0.036 4369 Dihedral : 9.662 69.935 5628 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.41 % Allowed : 5.77 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 2992 helix: 1.48 (0.21), residues: 690 sheet: 0.40 (0.19), residues: 681 loop : -0.78 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 353 HIS 0.003 0.001 HIS B 207 PHE 0.017 0.001 PHE A 906 TYR 0.022 0.001 TYR A 453 ARG 0.002 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 48) link_NAG-ASN : angle 2.14021 ( 144) link_ALPHA1-6 : bond 0.00796 ( 8) link_ALPHA1-6 : angle 2.01101 ( 24) link_BETA1-4 : bond 0.01660 ( 52) link_BETA1-4 : angle 4.48205 ( 156) link_ALPHA1-3 : bond 0.01364 ( 8) link_ALPHA1-3 : angle 2.49951 ( 24) hydrogen bonds : bond 0.03922 ( 961) hydrogen bonds : angle 4.95638 ( 2655) SS BOND : bond 0.00459 ( 38) SS BOND : angle 0.79224 ( 76) covalent geometry : bond 0.00364 (25967) covalent geometry : angle 0.54641 (35310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 2.783 Fit side-chains REVERT: C 460 ASN cc_start: 0.8118 (m-40) cc_final: 0.7729 (m110) outliers start: 11 outliers final: 8 residues processed: 56 average time/residue: 0.3211 time to fit residues: 33.2771 Evaluate side-chains 51 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 32 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 135 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 137 optimal weight: 50.0000 chunk 8 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.096331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.061801 restraints weight = 67041.742| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.41 r_work: 0.2875 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 26121 Z= 0.242 Angle : 0.705 18.475 35734 Z= 0.320 Chirality : 0.050 0.378 4365 Planarity : 0.004 0.035 4369 Dihedral : 9.259 66.385 5628 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.86 % Allowed : 6.78 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2992 helix: 1.37 (0.20), residues: 693 sheet: 0.24 (0.19), residues: 685 loop : -0.81 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 353 HIS 0.005 0.001 HIS B1058 PHE 0.024 0.002 PHE A 906 TYR 0.018 0.002 TYR A 423 ARG 0.005 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 48) link_NAG-ASN : angle 2.32462 ( 144) link_ALPHA1-6 : bond 0.00776 ( 8) link_ALPHA1-6 : angle 2.03954 ( 24) link_BETA1-4 : bond 0.01630 ( 52) link_BETA1-4 : angle 4.44698 ( 156) link_ALPHA1-3 : bond 0.01357 ( 8) link_ALPHA1-3 : angle 2.31912 ( 24) hydrogen bonds : bond 0.04831 ( 961) hydrogen bonds : angle 5.16076 ( 2655) SS BOND : bond 0.00491 ( 38) SS BOND : angle 1.13057 ( 76) covalent geometry : bond 0.00580 (25967) covalent geometry : angle 0.62008 (35310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 2.891 Fit side-chains REVERT: B 1094 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.8932 (m) REVERT: C 460 ASN cc_start: 0.8239 (m-40) cc_final: 0.7918 (m110) outliers start: 23 outliers final: 16 residues processed: 67 average time/residue: 0.3146 time to fit residues: 38.8643 Evaluate side-chains 60 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 240 optimal weight: 40.0000 chunk 27 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 297 optimal weight: 0.3980 chunk 289 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.097500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069208 restraints weight = 66524.420| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 4.14 r_work: 0.2864 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26121 Z= 0.140 Angle : 0.630 18.442 35734 Z= 0.278 Chirality : 0.047 0.358 4365 Planarity : 0.003 0.035 4369 Dihedral : 8.792 62.199 5628 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.71 % Allowed : 7.27 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 2992 helix: 1.70 (0.21), residues: 689 sheet: 0.27 (0.19), residues: 689 loop : -0.77 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 353 HIS 0.002 0.001 HIS C1058 PHE 0.019 0.001 PHE A 374 TYR 0.016 0.001 TYR C1067 ARG 0.002 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 48) link_NAG-ASN : angle 2.12456 ( 144) link_ALPHA1-6 : bond 0.00829 ( 8) link_ALPHA1-6 : angle 2.10086 ( 24) link_BETA1-4 : bond 0.01632 ( 52) link_BETA1-4 : angle 4.36599 ( 156) link_ALPHA1-3 : bond 0.01348 ( 8) link_ALPHA1-3 : angle 2.24218 ( 24) hydrogen bonds : bond 0.03878 ( 961) hydrogen bonds : angle 4.95736 ( 2655) SS BOND : bond 0.00310 ( 38) SS BOND : angle 0.83926 ( 76) covalent geometry : bond 0.00310 (25967) covalent geometry : angle 0.53996 (35310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 2.849 Fit side-chains REVERT: B 740 MET cc_start: 0.9288 (tpp) cc_final: 0.9065 (ttm) REVERT: B 1094 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8804 (m) outliers start: 19 outliers final: 12 residues processed: 63 average time/residue: 0.3194 time to fit residues: 37.3707 Evaluate side-chains 56 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 219 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 132 optimal weight: 50.0000 chunk 172 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 246 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.096416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.062044 restraints weight = 67278.006| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.39 r_work: 0.2857 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26121 Z= 0.225 Angle : 0.679 18.335 35734 Z= 0.306 Chirality : 0.049 0.366 4365 Planarity : 0.003 0.036 4369 Dihedral : 8.691 59.630 5628 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.79 % Allowed : 7.79 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2992 helix: 1.52 (0.21), residues: 694 sheet: 0.26 (0.19), residues: 684 loop : -0.81 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 353 HIS 0.004 0.001 HIS C1058 PHE 0.016 0.001 PHE C 906 TYR 0.017 0.002 TYR A 423 ARG 0.004 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 48) link_NAG-ASN : angle 2.24366 ( 144) link_ALPHA1-6 : bond 0.00837 ( 8) link_ALPHA1-6 : angle 2.09600 ( 24) link_BETA1-4 : bond 0.01623 ( 52) link_BETA1-4 : angle 4.37617 ( 156) link_ALPHA1-3 : bond 0.01288 ( 8) link_ALPHA1-3 : angle 2.23523 ( 24) hydrogen bonds : bond 0.04506 ( 961) hydrogen bonds : angle 5.06151 ( 2655) SS BOND : bond 0.00449 ( 38) SS BOND : angle 1.01874 ( 76) covalent geometry : bond 0.00537 (25967) covalent geometry : angle 0.59383 (35310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 2.744 Fit side-chains REVERT: B 1094 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.8957 (m) outliers start: 21 outliers final: 18 residues processed: 64 average time/residue: 0.2991 time to fit residues: 36.0573 Evaluate side-chains 63 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 68 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 302 optimal weight: 4.9990 chunk 171 optimal weight: 0.0970 chunk 218 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 279 optimal weight: 0.5980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.097223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.064067 restraints weight = 66436.730| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.31 r_work: 0.2877 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26121 Z= 0.145 Angle : 0.630 18.317 35734 Z= 0.279 Chirality : 0.047 0.355 4365 Planarity : 0.003 0.036 4369 Dihedral : 8.375 59.897 5628 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.94 % Allowed : 7.94 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2992 helix: 1.75 (0.21), residues: 692 sheet: 0.25 (0.19), residues: 682 loop : -0.74 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 353 HIS 0.002 0.001 HIS C1058 PHE 0.017 0.001 PHE A 374 TYR 0.027 0.001 TYR A 423 ARG 0.002 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 48) link_NAG-ASN : angle 2.09731 ( 144) link_ALPHA1-6 : bond 0.00891 ( 8) link_ALPHA1-6 : angle 2.13608 ( 24) link_BETA1-4 : bond 0.01616 ( 52) link_BETA1-4 : angle 4.32715 ( 156) link_ALPHA1-3 : bond 0.01302 ( 8) link_ALPHA1-3 : angle 2.08045 ( 24) hydrogen bonds : bond 0.03846 ( 961) hydrogen bonds : angle 4.91460 ( 2655) SS BOND : bond 0.00283 ( 38) SS BOND : angle 0.89059 ( 76) covalent geometry : bond 0.00328 (25967) covalent geometry : angle 0.54211 (35310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 3.057 Fit side-chains REVERT: B 1094 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8773 (m) outliers start: 25 outliers final: 21 residues processed: 66 average time/residue: 0.3366 time to fit residues: 41.7467 Evaluate side-chains 66 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 142 optimal weight: 0.0170 chunk 200 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 155 optimal weight: 0.0010 chunk 106 optimal weight: 9.9990 chunk 259 optimal weight: 0.0870 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.098876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.070965 restraints weight = 66538.249| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.86 r_work: 0.2914 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26121 Z= 0.102 Angle : 0.598 18.224 35734 Z= 0.261 Chirality : 0.046 0.349 4365 Planarity : 0.003 0.037 4369 Dihedral : 7.847 58.296 5628 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.67 % Allowed : 8.32 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 2992 helix: 2.11 (0.21), residues: 677 sheet: 0.41 (0.19), residues: 681 loop : -0.65 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP A 353 HIS 0.002 0.000 HIS B 207 PHE 0.017 0.001 PHE C 456 TYR 0.018 0.001 TYR A 423 ARG 0.002 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 48) link_NAG-ASN : angle 1.95874 ( 144) link_ALPHA1-6 : bond 0.00956 ( 8) link_ALPHA1-6 : angle 2.14369 ( 24) link_BETA1-4 : bond 0.01647 ( 52) link_BETA1-4 : angle 4.26983 ( 156) link_ALPHA1-3 : bond 0.01275 ( 8) link_ALPHA1-3 : angle 1.88377 ( 24) hydrogen bonds : bond 0.03068 ( 961) hydrogen bonds : angle 4.64335 ( 2655) SS BOND : bond 0.00164 ( 38) SS BOND : angle 0.61714 ( 76) covalent geometry : bond 0.00197 (25967) covalent geometry : angle 0.50969 (35310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 2.797 Fit side-chains REVERT: B 740 MET cc_start: 0.8846 (ttm) cc_final: 0.8597 (ttt) outliers start: 18 outliers final: 13 residues processed: 63 average time/residue: 0.3078 time to fit residues: 36.2795 Evaluate side-chains 60 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 263 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 131 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.097558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.064100 restraints weight = 66417.636| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.37 r_work: 0.2885 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26121 Z= 0.149 Angle : 0.618 18.146 35734 Z= 0.273 Chirality : 0.047 0.350 4365 Planarity : 0.003 0.035 4369 Dihedral : 7.805 59.264 5628 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.56 % Allowed : 8.54 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2992 helix: 2.06 (0.21), residues: 686 sheet: 0.35 (0.19), residues: 686 loop : -0.62 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 353 HIS 0.003 0.001 HIS C1058 PHE 0.012 0.001 PHE A 374 TYR 0.023 0.001 TYR A 423 ARG 0.003 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 48) link_NAG-ASN : angle 2.03834 ( 144) link_ALPHA1-6 : bond 0.00945 ( 8) link_ALPHA1-6 : angle 2.12987 ( 24) link_BETA1-4 : bond 0.01617 ( 52) link_BETA1-4 : angle 4.26945 ( 156) link_ALPHA1-3 : bond 0.01184 ( 8) link_ALPHA1-3 : angle 1.90720 ( 24) hydrogen bonds : bond 0.03730 ( 961) hydrogen bonds : angle 4.74249 ( 2655) SS BOND : bond 0.00288 ( 38) SS BOND : angle 0.79244 ( 76) covalent geometry : bond 0.00338 (25967) covalent geometry : angle 0.53106 (35310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5984 Ramachandran restraints generated. 2992 Oldfield, 0 Emsley, 2992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 2.963 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 60 average time/residue: 0.3210 time to fit residues: 36.5826 Evaluate side-chains 59 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 164 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 280 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 201 optimal weight: 0.5980 chunk 290 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.098257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070276 restraints weight = 66242.528| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.94 r_work: 0.2893 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26121 Z= 0.109 Angle : 0.598 18.182 35734 Z= 0.262 Chirality : 0.046 0.347 4365 Planarity : 0.003 0.035 4369 Dihedral : 7.626 58.620 5628 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.49 % Allowed : 8.62 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 2992 helix: 2.18 (0.21), residues: 686 sheet: 0.42 (0.19), residues: 682 loop : -0.58 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 353 HIS 0.002 0.000 HIS B 207 PHE 0.016 0.001 PHE C 456 TYR 0.022 0.001 TYR A 423 ARG 0.003 0.000 ARG A1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 48) link_NAG-ASN : angle 1.95819 ( 144) link_ALPHA1-6 : bond 0.00980 ( 8) link_ALPHA1-6 : angle 2.13884 ( 24) link_BETA1-4 : bond 0.01635 ( 52) link_BETA1-4 : angle 4.24803 ( 156) link_ALPHA1-3 : bond 0.01193 ( 8) link_ALPHA1-3 : angle 1.78122 ( 24) hydrogen bonds : bond 0.03324 ( 961) hydrogen bonds : angle 4.66109 ( 2655) SS BOND : bond 0.00198 ( 38) SS BOND : angle 0.67403 ( 76) covalent geometry : bond 0.00224 (25967) covalent geometry : angle 0.51012 (35310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12280.59 seconds wall clock time: 211 minutes 43.21 seconds (12703.21 seconds total)