Starting phenix.real_space_refine on Sun Jun 22 00:46:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8epn_28531/06_2025/8epn_28531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8epn_28531/06_2025/8epn_28531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8epn_28531/06_2025/8epn_28531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8epn_28531/06_2025/8epn_28531.map" model { file = "/net/cci-nas-00/data/ceres_data/8epn_28531/06_2025/8epn_28531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8epn_28531/06_2025/8epn_28531.cif" } resolution = 2.8 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= 0.000 sd= 0.002 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 99 5.16 5 C 15915 2.51 5 N 3993 2.21 5 O 5070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 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: 25077 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 Chain: "B" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 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: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 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: 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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 Time building chain proxies: 17.17, per 1000 atoms: 0.68 Number of scatterers: 25077 At special positions: 0 Unit cell: (145.39, 143.38, 175.54, 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 99 16.00 O 5070 8.00 N 3993 7.00 C 15915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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 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 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 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 B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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 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 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 E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA L 3 " - " MAN L 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA L 3 " - " MAN L 5 " " BMA P 3 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 5 " " BMA W 3 " - " MAN W 5 " " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA h 3 " - " MAN h 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1201 " - " ASN A 709 " " NAG A1202 " - " ASN A 603 " " NAG A1203 " - " ASN A 165 " " NAG A1204 " - " ASN A 61 " " NAG A1205 " - " ASN A 234 " " NAG B1201 " - " ASN B 709 " " NAG B1202 " - " ASN B 603 " " NAG B1203 " - " ASN B 165 " " NAG B1204 " - " ASN B 61 " " NAG B1205 " - " ASN B 234 " " NAG C1201 " - " ASN C 709 " " NAG C1202 " - " ASN C 603 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 234 " " NAG D 1 " - " ASN A 616 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A 657 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A 331 " " NAG O 1 " - " ASN B 616 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B 657 " " NAG U 1 " - " ASN B 122 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN B1074 " " NAG Y 1 " - " ASN B 331 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 282 " " NAG c 1 " - " ASN C 343 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C 657 " " NAG f 1 " - " ASN C 122 " " NAG g 1 " - " ASN C1098 " " NAG h 1 " - " ASN C1134 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C 331 " Time building additional restraints: 7.44 Conformation dependent library (CDL) restraints added in 3.1 seconds 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 43 sheets defined 26.5% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 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 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.108A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.967A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.518A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.635A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.518A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.540A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.530A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.290A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.076A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.295A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.113A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.525A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.641A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.511A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.512A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.514A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.296A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.072A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.302A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.163A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.532A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.654A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.517A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.542A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.303A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.074A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.301A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 5.841A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.114A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.725A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.930A 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 removed outlier: 3.813A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.938A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.072A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.120A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.029A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.579A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.827A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.270A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.968A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 5.926A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.730A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.753A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.607A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.043A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.118A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.048A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.581A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.786A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.249A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 5.907A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.707A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.691A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.678A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.869A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.077A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.008A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.586A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.816A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.272A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1081 through 1082 1007 hydrogen bonds defined for protein. 2757 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: 11.24 Time building geometry restraints manager: 8.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7757 1.34 - 1.46: 6330 1.46 - 1.58: 11395 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 25605 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" N THR C 393 " pdb=" CA THR C 393 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 7.16e+00 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.89e+00 ... (remaining 25600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 34064 2.33 - 4.67: 648 4.67 - 7.00: 108 7.00 - 9.33: 1 9.33 - 11.66: 3 Bond angle restraints: 34824 Sorted by residual: angle pdb=" C ASN A1135 " pdb=" N THR A1136 " pdb=" CA THR A1136 " ideal model delta sigma weight residual 121.70 133.36 -11.66 1.80e+00 3.09e-01 4.20e+01 angle pdb=" C ASN C1135 " pdb=" N THR C1136 " pdb=" CA THR C1136 " ideal model delta sigma weight residual 121.70 133.32 -11.62 1.80e+00 3.09e-01 4.17e+01 angle pdb=" C ASN B1135 " pdb=" N THR B1136 " pdb=" CA THR B1136 " ideal model delta sigma weight residual 121.70 133.30 -11.60 1.80e+00 3.09e-01 4.15e+01 angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 117.23 111.18 6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" C ASN C 87 " pdb=" CA ASN C 87 " pdb=" CB ASN C 87 " ideal model delta sigma weight residual 117.23 111.20 6.03 1.36e+00 5.41e-01 1.97e+01 ... (remaining 34819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 15660 24.98 - 49.96: 826 49.96 - 74.94: 162 74.94 - 99.93: 134 99.93 - 124.91: 51 Dihedral angle restraints: 16833 sinusoidal: 8118 harmonic: 8715 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -163.41 77.41 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -161.99 75.99 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -161.95 75.95 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 16830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3685 0.072 - 0.144: 611 0.144 - 0.215: 12 0.215 - 0.287: 13 0.287 - 0.359: 14 Chirality restraints: 4335 Sorted by residual: chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 4332 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B1132 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C ILE B1132 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE B1132 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B1133 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C1132 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ILE C1132 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE C1132 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL C1133 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 138 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.01e+00 pdb=" N PRO A 139 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.024 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2685 2.75 - 3.29: 23064 3.29 - 3.83: 39662 3.83 - 4.36: 45309 4.36 - 4.90: 79566 Nonbonded interactions: 190286 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.243 3.040 nonbonded pdb=" NZ LYS C 825 " pdb=" O THR C 941 " model vdw 2.269 3.120 ... (remaining 190281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'W' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' } 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: 10.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 1.160 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 61.870 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25758 Z= 0.238 Angle : 0.790 11.663 35256 Z= 0.363 Chirality : 0.053 0.359 4335 Planarity : 0.004 0.043 4314 Dihedral : 18.173 124.907 11130 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.84 % Allowed : 12.38 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: -0.10 (0.15), residues: 2931 helix: 1.64 (0.21), residues: 669 sheet: 0.67 (0.21), residues: 543 loop : -1.06 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 353 HIS 0.004 0.001 HIS B 207 PHE 0.018 0.001 PHE A 140 TYR 0.021 0.001 TYR A 453 ARG 0.008 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 48) link_NAG-ASN : angle 3.14943 ( 144) link_ALPHA1-6 : bond 0.00614 ( 15) link_ALPHA1-6 : angle 1.58007 ( 45) link_BETA1-4 : bond 0.00545 ( 48) link_BETA1-4 : angle 2.03902 ( 144) link_ALPHA1-3 : bond 0.00427 ( 15) link_ALPHA1-3 : angle 1.75971 ( 45) hydrogen bonds : bond 0.21895 ( 1001) hydrogen bonds : angle 8.34392 ( 2757) SS BOND : bond 0.00275 ( 27) SS BOND : angle 1.05999 ( 54) covalent geometry : bond 0.00486 (25605) covalent geometry : angle 0.75109 (34824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 PHE cc_start: 0.7629 (m-80) cc_final: 0.7167 (m-80) REVERT: C 133 PHE cc_start: 0.7579 (m-80) cc_final: 0.7115 (m-80) outliers start: 22 outliers final: 19 residues processed: 116 average time/residue: 1.0375 time to fit residues: 147.7929 Evaluate side-chains 92 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 151 optimal weight: 0.0030 chunk 120 optimal weight: 0.0670 chunk 232 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 141 optimal weight: 0.0980 chunk 173 optimal weight: 0.0030 chunk 269 optimal weight: 0.2980 overall best weight: 0.0938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 121 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.122236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.077472 restraints weight = 60859.662| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 4.12 r_work: 0.3100 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25758 Z= 0.126 Angle : 0.622 8.868 35256 Z= 0.298 Chirality : 0.048 0.342 4335 Planarity : 0.004 0.041 4314 Dihedral : 13.685 110.358 5786 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.72 % Allowed : 11.15 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.14 (0.15), residues: 2931 helix: 2.12 (0.21), residues: 669 sheet: 0.94 (0.22), residues: 531 loop : -1.07 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 PHE 0.015 0.001 PHE C 400 TYR 0.017 0.001 TYR A1067 ARG 0.006 0.000 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 48) link_NAG-ASN : angle 2.76301 ( 144) link_ALPHA1-6 : bond 0.00930 ( 15) link_ALPHA1-6 : angle 1.87959 ( 45) link_BETA1-4 : bond 0.00537 ( 48) link_BETA1-4 : angle 1.92621 ( 144) link_ALPHA1-3 : bond 0.01059 ( 15) link_ALPHA1-3 : angle 2.49980 ( 45) hydrogen bonds : bond 0.05634 ( 1001) hydrogen bonds : angle 6.21080 ( 2757) SS BOND : bond 0.00278 ( 27) SS BOND : angle 0.67164 ( 54) covalent geometry : bond 0.00243 (25605) covalent geometry : angle 0.57603 (34824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 4.246 Fit side-chains REVERT: A 707 TYR cc_start: 0.8174 (m-80) cc_final: 0.7828 (m-10) REVERT: B 133 PHE cc_start: 0.7639 (m-80) cc_final: 0.7027 (m-80) REVERT: B 957 GLN cc_start: 0.8749 (tt0) cc_final: 0.8522 (tt0) REVERT: C 133 PHE cc_start: 0.7641 (m-80) cc_final: 0.7007 (m-80) REVERT: C 239 GLN cc_start: 0.7366 (tp-100) cc_final: 0.7164 (tp40) REVERT: C 386 LYS cc_start: 0.7854 (mttt) cc_final: 0.7102 (mtpt) REVERT: C 979 ASP cc_start: 0.8074 (t70) cc_final: 0.7866 (t0) outliers start: 45 outliers final: 16 residues processed: 141 average time/residue: 1.0916 time to fit residues: 194.0379 Evaluate side-chains 95 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 204 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 chunk 150 optimal weight: 0.0670 chunk 156 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 286 optimal weight: 4.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.119266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073067 restraints weight = 60100.385| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.09 r_work: 0.2989 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25758 Z= 0.230 Angle : 0.687 9.715 35256 Z= 0.333 Chirality : 0.051 0.353 4335 Planarity : 0.005 0.044 4314 Dihedral : 12.842 115.169 5765 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.07 % Allowed : 11.69 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.07 (0.15), residues: 2931 helix: 1.95 (0.21), residues: 687 sheet: 0.78 (0.21), residues: 573 loop : -1.09 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 436 HIS 0.006 0.001 HIS B1058 PHE 0.019 0.002 PHE A 140 TYR 0.021 0.002 TYR C1067 ARG 0.005 0.001 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 48) link_NAG-ASN : angle 2.91271 ( 144) link_ALPHA1-6 : bond 0.01048 ( 15) link_ALPHA1-6 : angle 1.92652 ( 45) link_BETA1-4 : bond 0.00468 ( 48) link_BETA1-4 : angle 1.68093 ( 144) link_ALPHA1-3 : bond 0.01150 ( 15) link_ALPHA1-3 : angle 1.54724 ( 45) hydrogen bonds : bond 0.08341 ( 1001) hydrogen bonds : angle 6.08425 ( 2757) SS BOND : bond 0.00338 ( 27) SS BOND : angle 0.85819 ( 54) covalent geometry : bond 0.00556 (25605) covalent geometry : angle 0.64939 (34824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 83 time to evaluate : 4.808 Fit side-chains revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8817 (t) cc_final: 0.8538 (p) REVERT: A 707 TYR cc_start: 0.8243 (m-80) cc_final: 0.8036 (m-10) REVERT: B 133 PHE cc_start: 0.7798 (m-80) cc_final: 0.7220 (m-80) REVERT: B 227 VAL cc_start: 0.8855 (t) cc_final: 0.8545 (p) REVERT: C 133 PHE cc_start: 0.7654 (m-80) cc_final: 0.7161 (m-80) REVERT: C 314 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8198 (tp40) outliers start: 54 outliers final: 16 residues processed: 129 average time/residue: 1.2858 time to fit residues: 209.7308 Evaluate side-chains 87 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 174 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 280 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.120807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.074795 restraints weight = 60710.288| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 4.23 r_work: 0.3026 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25758 Z= 0.133 Angle : 0.609 9.686 35256 Z= 0.286 Chirality : 0.048 0.331 4335 Planarity : 0.004 0.042 4314 Dihedral : 11.416 113.002 5763 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.15 % Allowed : 11.80 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.15 (0.15), residues: 2931 helix: 2.15 (0.21), residues: 684 sheet: 0.81 (0.22), residues: 570 loop : -1.09 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS A1064 PHE 0.015 0.001 PHE A 140 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 48) link_NAG-ASN : angle 2.73332 ( 144) link_ALPHA1-6 : bond 0.01135 ( 15) link_ALPHA1-6 : angle 1.87790 ( 45) link_BETA1-4 : bond 0.00460 ( 48) link_BETA1-4 : angle 1.65060 ( 144) link_ALPHA1-3 : bond 0.01202 ( 15) link_ALPHA1-3 : angle 1.56606 ( 45) hydrogen bonds : bond 0.06432 ( 1001) hydrogen bonds : angle 5.69255 ( 2757) SS BOND : bond 0.00305 ( 27) SS BOND : angle 0.58945 ( 54) covalent geometry : bond 0.00289 (25605) covalent geometry : angle 0.57039 (34824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 83 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8793 (t) cc_final: 0.8529 (p) REVERT: A 314 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8257 (tp40) REVERT: B 133 PHE cc_start: 0.7779 (m-80) cc_final: 0.7187 (m-80) REVERT: B 227 VAL cc_start: 0.8842 (t) cc_final: 0.8536 (p) REVERT: B 314 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: B 707 TYR cc_start: 0.8231 (m-80) cc_final: 0.7849 (m-10) REVERT: B 957 GLN cc_start: 0.8788 (tt0) cc_final: 0.8554 (tt0) REVERT: C 133 PHE cc_start: 0.7654 (m-80) cc_final: 0.7153 (m-80) REVERT: C 239 GLN cc_start: 0.7149 (tp40) cc_final: 0.6789 (mm-40) REVERT: C 314 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8111 (tp40) REVERT: C 380 TYR cc_start: 0.5941 (m-10) cc_final: 0.5673 (m-10) REVERT: C 740 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8317 (tpt) outliers start: 56 outliers final: 27 residues processed: 134 average time/residue: 0.9250 time to fit residues: 155.3724 Evaluate side-chains 103 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 49 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 249 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 220 optimal weight: 0.3980 chunk 101 optimal weight: 10.0000 chunk 257 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** 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 = 0.4075 r_free = 0.4075 target = 0.120420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.073991 restraints weight = 60184.228| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.19 r_work: 0.2999 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25758 Z= 0.175 Angle : 0.640 9.800 35256 Z= 0.303 Chirality : 0.049 0.341 4335 Planarity : 0.004 0.044 4314 Dihedral : 10.669 114.173 5761 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.45 % Allowed : 12.07 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.14 (0.15), residues: 2931 helix: 2.11 (0.21), residues: 687 sheet: 0.83 (0.21), residues: 573 loop : -1.10 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 353 HIS 0.004 0.001 HIS A1064 PHE 0.020 0.001 PHE B 400 TYR 0.020 0.001 TYR A 707 ARG 0.002 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 48) link_NAG-ASN : angle 2.79090 ( 144) link_ALPHA1-6 : bond 0.01222 ( 15) link_ALPHA1-6 : angle 2.00173 ( 45) link_BETA1-4 : bond 0.00439 ( 48) link_BETA1-4 : angle 1.64057 ( 144) link_ALPHA1-3 : bond 0.01240 ( 15) link_ALPHA1-3 : angle 1.46130 ( 45) hydrogen bonds : bond 0.07248 ( 1001) hydrogen bonds : angle 5.67763 ( 2757) SS BOND : bond 0.00321 ( 27) SS BOND : angle 1.00424 ( 54) covalent geometry : bond 0.00408 (25605) covalent geometry : angle 0.60158 (34824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 82 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8830 (t) cc_final: 0.8562 (p) REVERT: A 314 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8277 (tp40) REVERT: B 133 PHE cc_start: 0.7789 (m-80) cc_final: 0.7282 (m-80) REVERT: B 227 VAL cc_start: 0.8858 (t) cc_final: 0.8553 (p) REVERT: B 314 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8188 (tm-30) REVERT: B 707 TYR cc_start: 0.8265 (m-80) cc_final: 0.7948 (m-10) REVERT: B 957 GLN cc_start: 0.8833 (tt0) cc_final: 0.8601 (tt0) REVERT: C 133 PHE cc_start: 0.7657 (m-80) cc_final: 0.7202 (m-80) REVERT: C 227 VAL cc_start: 0.8830 (t) cc_final: 0.8559 (p) REVERT: C 239 GLN cc_start: 0.7249 (tp40) cc_final: 0.6693 (mm-40) REVERT: C 314 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8226 (tp40) REVERT: C 380 TYR cc_start: 0.6042 (m-10) cc_final: 0.5837 (m-10) REVERT: C 740 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8334 (tpt) REVERT: C 1144 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7715 (mm-30) outliers start: 64 outliers final: 29 residues processed: 141 average time/residue: 0.9524 time to fit residues: 166.4389 Evaluate side-chains 111 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 206 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 294 optimal weight: 0.3980 chunk 50 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.120026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073632 restraints weight = 60484.567| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 4.20 r_work: 0.2992 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25758 Z= 0.184 Angle : 0.651 9.835 35256 Z= 0.309 Chirality : 0.049 0.340 4335 Planarity : 0.004 0.043 4314 Dihedral : 9.816 114.055 5761 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.53 % Allowed : 12.11 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.18 (0.15), residues: 2931 helix: 2.18 (0.21), residues: 669 sheet: 1.04 (0.22), residues: 531 loop : -1.08 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.004 0.001 HIS A1064 PHE 0.016 0.002 PHE A 400 TYR 0.020 0.001 TYR A 453 ARG 0.011 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 48) link_NAG-ASN : angle 2.78534 ( 144) link_ALPHA1-6 : bond 0.01370 ( 15) link_ALPHA1-6 : angle 2.07333 ( 45) link_BETA1-4 : bond 0.00450 ( 48) link_BETA1-4 : angle 1.68197 ( 144) link_ALPHA1-3 : bond 0.01264 ( 15) link_ALPHA1-3 : angle 1.36973 ( 45) hydrogen bonds : bond 0.07389 ( 1001) hydrogen bonds : angle 5.65541 ( 2757) SS BOND : bond 0.00344 ( 27) SS BOND : angle 0.83023 ( 54) covalent geometry : bond 0.00430 (25605) covalent geometry : angle 0.61305 (34824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 86 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8843 (t) cc_final: 0.8585 (p) REVERT: A 314 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8297 (tp40) REVERT: B 133 PHE cc_start: 0.7784 (m-80) cc_final: 0.7252 (m-80) REVERT: B 190 ARG cc_start: 0.7591 (ttp-170) cc_final: 0.7034 (ttm110) REVERT: B 227 VAL cc_start: 0.8837 (t) cc_final: 0.8548 (p) REVERT: B 314 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: B 707 TYR cc_start: 0.8280 (m-80) cc_final: 0.7996 (m-10) REVERT: B 794 ILE cc_start: 0.7526 (pt) cc_final: 0.7296 (mm) REVERT: C 133 PHE cc_start: 0.7624 (m-80) cc_final: 0.7239 (m-80) REVERT: C 239 GLN cc_start: 0.7344 (tp40) cc_final: 0.6608 (tp40) REVERT: C 314 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8262 (tp40) REVERT: C 380 TYR cc_start: 0.6163 (m-10) cc_final: 0.5929 (m-10) REVERT: C 425 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6670 (tt) REVERT: C 740 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8330 (tpt) REVERT: C 1144 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7782 (mm-30) outliers start: 66 outliers final: 36 residues processed: 146 average time/residue: 0.8698 time to fit residues: 160.3964 Evaluate side-chains 120 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 270 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.120299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.074539 restraints weight = 60907.478| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.09 r_work: 0.3012 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25758 Z= 0.150 Angle : 0.620 9.838 35256 Z= 0.292 Chirality : 0.048 0.332 4335 Planarity : 0.004 0.044 4314 Dihedral : 9.160 113.017 5761 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.07 % Allowed : 12.61 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.26 (0.15), residues: 2931 helix: 2.27 (0.21), residues: 666 sheet: 1.05 (0.22), residues: 531 loop : -1.03 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 353 HIS 0.003 0.001 HIS A1064 PHE 0.026 0.001 PHE B 400 TYR 0.021 0.001 TYR A 453 ARG 0.005 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 48) link_NAG-ASN : angle 2.71004 ( 144) link_ALPHA1-6 : bond 0.01360 ( 15) link_ALPHA1-6 : angle 1.99528 ( 45) link_BETA1-4 : bond 0.00459 ( 48) link_BETA1-4 : angle 1.70660 ( 144) link_ALPHA1-3 : bond 0.01253 ( 15) link_ALPHA1-3 : angle 1.28222 ( 45) hydrogen bonds : bond 0.06821 ( 1001) hydrogen bonds : angle 5.54409 ( 2757) SS BOND : bond 0.00308 ( 27) SS BOND : angle 0.67392 ( 54) covalent geometry : bond 0.00336 (25605) covalent geometry : angle 0.58172 (34824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 93 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.6687 (OUTLIER) cc_final: 0.6364 (m-70) REVERT: A 227 VAL cc_start: 0.8842 (t) cc_final: 0.8586 (p) REVERT: A 314 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8296 (tp40) REVERT: B 133 PHE cc_start: 0.7787 (m-80) cc_final: 0.7231 (m-80) REVERT: B 190 ARG cc_start: 0.7562 (ttp-170) cc_final: 0.7005 (ttm110) REVERT: B 227 VAL cc_start: 0.8833 (t) cc_final: 0.8553 (p) REVERT: B 314 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: B 707 TYR cc_start: 0.8269 (m-80) cc_final: 0.7981 (m-10) REVERT: B 794 ILE cc_start: 0.7546 (pt) cc_final: 0.7337 (mm) REVERT: B 957 GLN cc_start: 0.8815 (tt0) cc_final: 0.8589 (tt0) REVERT: C 133 PHE cc_start: 0.7643 (m-80) cc_final: 0.7221 (m-80) REVERT: C 239 GLN cc_start: 0.7347 (tp40) cc_final: 0.6780 (mm-40) REVERT: C 314 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8235 (tp40) REVERT: C 380 TYR cc_start: 0.6158 (m-10) cc_final: 0.5941 (m-10) REVERT: C 740 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8305 (tpt) REVERT: C 1144 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7796 (mm-30) outliers start: 54 outliers final: 41 residues processed: 144 average time/residue: 0.8946 time to fit residues: 161.5936 Evaluate side-chains 128 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 82 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 290 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 283 optimal weight: 3.9990 chunk 225 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 271 optimal weight: 0.0000 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** 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 = 0.4097 r_free = 0.4097 target = 0.121567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.076209 restraints weight = 60515.295| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.08 r_work: 0.3058 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25758 Z= 0.118 Angle : 0.585 9.870 35256 Z= 0.273 Chirality : 0.046 0.327 4335 Planarity : 0.004 0.041 4314 Dihedral : 8.373 111.204 5761 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.72 % Allowed : 13.30 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.38 (0.15), residues: 2931 helix: 2.43 (0.21), residues: 666 sheet: 1.11 (0.22), residues: 525 loop : -0.96 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.002 0.000 HIS C1064 PHE 0.024 0.001 PHE B 541 TYR 0.015 0.001 TYR A1067 ARG 0.004 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 48) link_NAG-ASN : angle 2.61973 ( 144) link_ALPHA1-6 : bond 0.01359 ( 15) link_ALPHA1-6 : angle 1.92721 ( 45) link_BETA1-4 : bond 0.00497 ( 48) link_BETA1-4 : angle 1.69484 ( 144) link_ALPHA1-3 : bond 0.01254 ( 15) link_ALPHA1-3 : angle 1.16218 ( 45) hydrogen bonds : bond 0.05690 ( 1001) hydrogen bonds : angle 5.30588 ( 2757) SS BOND : bond 0.00286 ( 27) SS BOND : angle 0.58836 ( 54) covalent geometry : bond 0.00244 (25605) covalent geometry : angle 0.54726 (34824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 96 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8822 (t) cc_final: 0.8579 (p) REVERT: A 314 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8302 (tp40) REVERT: A 386 LYS cc_start: 0.7562 (mttt) cc_final: 0.7334 (mttt) REVERT: B 133 PHE cc_start: 0.7724 (m-80) cc_final: 0.7147 (m-80) REVERT: B 227 VAL cc_start: 0.8829 (t) cc_final: 0.8561 (p) REVERT: B 314 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: B 707 TYR cc_start: 0.8220 (m-80) cc_final: 0.7884 (m-10) REVERT: B 794 ILE cc_start: 0.7493 (pt) cc_final: 0.7284 (mm) REVERT: B 957 GLN cc_start: 0.8793 (tt0) cc_final: 0.8575 (tt0) REVERT: C 133 PHE cc_start: 0.7616 (m-80) cc_final: 0.7204 (m-80) REVERT: C 227 VAL cc_start: 0.8808 (t) cc_final: 0.8571 (p) REVERT: C 239 GLN cc_start: 0.7285 (tp40) cc_final: 0.6728 (mm-40) REVERT: C 314 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8175 (tp40) REVERT: C 740 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8287 (tpt) REVERT: C 1144 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7779 (mm-30) outliers start: 45 outliers final: 36 residues processed: 136 average time/residue: 0.9661 time to fit residues: 164.5932 Evaluate side-chains 125 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 102 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 chunk 141 optimal weight: 0.0070 chunk 251 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 289 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 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 = 0.4101 r_free = 0.4101 target = 0.122056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.076430 restraints weight = 60677.750| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.24 r_work: 0.3062 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25758 Z= 0.112 Angle : 0.579 9.830 35256 Z= 0.270 Chirality : 0.046 0.326 4335 Planarity : 0.004 0.040 4314 Dihedral : 8.127 110.920 5761 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.69 % Allowed : 13.49 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.46 (0.15), residues: 2931 helix: 2.56 (0.21), residues: 663 sheet: 1.14 (0.22), residues: 519 loop : -0.91 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 353 HIS 0.002 0.000 HIS A1064 PHE 0.020 0.001 PHE A 541 TYR 0.019 0.001 TYR C 453 ARG 0.004 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 48) link_NAG-ASN : angle 2.57884 ( 144) link_ALPHA1-6 : bond 0.01322 ( 15) link_ALPHA1-6 : angle 1.91511 ( 45) link_BETA1-4 : bond 0.00493 ( 48) link_BETA1-4 : angle 1.69641 ( 144) link_ALPHA1-3 : bond 0.01216 ( 15) link_ALPHA1-3 : angle 1.16294 ( 45) hydrogen bonds : bond 0.05502 ( 1001) hydrogen bonds : angle 5.24104 ( 2757) SS BOND : bond 0.00265 ( 27) SS BOND : angle 0.56890 ( 54) covalent geometry : bond 0.00227 (25605) covalent geometry : angle 0.54095 (34824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 4.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.6202 (m-70) REVERT: A 227 VAL cc_start: 0.8821 (t) cc_final: 0.8577 (p) REVERT: A 314 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8295 (tp40) REVERT: A 386 LYS cc_start: 0.7552 (mttt) cc_final: 0.7333 (mttt) REVERT: B 133 PHE cc_start: 0.7738 (m-80) cc_final: 0.7146 (m-80) REVERT: B 227 VAL cc_start: 0.8817 (t) cc_final: 0.8552 (p) REVERT: B 314 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: B 707 TYR cc_start: 0.8216 (m-80) cc_final: 0.7884 (m-10) REVERT: B 957 GLN cc_start: 0.8798 (tt0) cc_final: 0.8579 (tt0) REVERT: C 133 PHE cc_start: 0.7620 (m-80) cc_final: 0.7202 (m-80) REVERT: C 227 VAL cc_start: 0.8820 (t) cc_final: 0.8587 (p) REVERT: C 239 GLN cc_start: 0.7292 (tp40) cc_final: 0.6727 (mm-40) REVERT: C 386 LYS cc_start: 0.7379 (mttt) cc_final: 0.7083 (ptpt) REVERT: C 740 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8250 (tpt) REVERT: C 1144 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7787 (mm-30) outliers start: 44 outliers final: 33 residues processed: 133 average time/residue: 0.9823 time to fit residues: 166.0921 Evaluate side-chains 119 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 152 optimal weight: 4.9990 chunk 245 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 280 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** 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 = 0.4055 r_free = 0.4055 target = 0.119227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.072988 restraints weight = 60453.671| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 4.09 r_work: 0.2973 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 25758 Z= 0.257 Angle : 0.692 9.953 35256 Z= 0.334 Chirality : 0.051 0.354 4335 Planarity : 0.004 0.044 4314 Dihedral : 8.474 114.447 5761 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.84 % Allowed : 13.60 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.22 (0.15), residues: 2931 helix: 2.17 (0.21), residues: 669 sheet: 1.01 (0.22), residues: 525 loop : -1.01 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 353 HIS 0.006 0.001 HIS B1058 PHE 0.026 0.002 PHE C 541 TYR 0.023 0.002 TYR B 453 ARG 0.005 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 48) link_NAG-ASN : angle 2.72130 ( 144) link_ALPHA1-6 : bond 0.01393 ( 15) link_ALPHA1-6 : angle 2.13953 ( 45) link_BETA1-4 : bond 0.00451 ( 48) link_BETA1-4 : angle 1.75388 ( 144) link_ALPHA1-3 : bond 0.01161 ( 15) link_ALPHA1-3 : angle 1.36754 ( 45) hydrogen bonds : bond 0.08236 ( 1001) hydrogen bonds : angle 5.69174 ( 2757) SS BOND : bond 0.00382 ( 27) SS BOND : angle 0.85655 ( 54) covalent geometry : bond 0.00620 (25605) covalent geometry : angle 0.65696 (34824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 88 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8850 (t) cc_final: 0.8596 (p) REVERT: A 314 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: A 386 LYS cc_start: 0.7712 (mttt) cc_final: 0.7456 (mttt) REVERT: B 133 PHE cc_start: 0.7815 (m-80) cc_final: 0.7303 (m-80) REVERT: B 227 VAL cc_start: 0.8856 (t) cc_final: 0.8577 (p) REVERT: C 133 PHE cc_start: 0.7621 (m-80) cc_final: 0.7276 (m-80) REVERT: C 227 VAL cc_start: 0.8855 (t) cc_final: 0.8604 (p) REVERT: C 314 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8249 (tp40) REVERT: C 386 LYS cc_start: 0.7542 (mttt) cc_final: 0.7117 (ptpp) REVERT: C 1144 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7811 (mm-30) outliers start: 48 outliers final: 29 residues processed: 134 average time/residue: 1.3938 time to fit residues: 231.4757 Evaluate side-chains 110 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 4.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 160 optimal weight: 0.6980 chunk 264 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** 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 = 0.4091 r_free = 0.4091 target = 0.121505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075611 restraints weight = 60018.234| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.22 r_work: 0.3042 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25758 Z= 0.119 Angle : 0.593 9.854 35256 Z= 0.280 Chirality : 0.046 0.318 4335 Planarity : 0.004 0.041 4314 Dihedral : 8.042 111.682 5761 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.15 % Allowed : 14.44 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.33 (0.15), residues: 2931 helix: 2.37 (0.21), residues: 666 sheet: 1.00 (0.22), residues: 534 loop : -0.96 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 353 HIS 0.002 0.001 HIS A1064 PHE 0.018 0.001 PHE A 238 TYR 0.019 0.001 TYR C 453 ARG 0.004 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 48) link_NAG-ASN : angle 2.57316 ( 144) link_ALPHA1-6 : bond 0.01349 ( 15) link_ALPHA1-6 : angle 1.94187 ( 45) link_BETA1-4 : bond 0.00516 ( 48) link_BETA1-4 : angle 1.73546 ( 144) link_ALPHA1-3 : bond 0.01215 ( 15) link_ALPHA1-3 : angle 1.16823 ( 45) hydrogen bonds : bond 0.05914 ( 1001) hydrogen bonds : angle 5.34238 ( 2757) SS BOND : bond 0.00269 ( 27) SS BOND : angle 0.59197 ( 54) covalent geometry : bond 0.00243 (25605) covalent geometry : angle 0.55626 (34824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20222.88 seconds wall clock time: 356 minutes 47.25 seconds (21407.25 seconds total)