Starting phenix.real_space_refine on Mon May 26 23:24:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gjm_40094/05_2025/8gjm_40094_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gjm_40094/05_2025/8gjm_40094.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/8gjm_40094/05_2025/8gjm_40094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gjm_40094/05_2025/8gjm_40094.map" model { file = "/net/cci-nas-00/data/ceres_data/8gjm_40094/05_2025/8gjm_40094_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gjm_40094/05_2025/8gjm_40094_neut.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= 0.011 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 123 5.16 5 C 18231 2.51 5 N 4653 2.21 5 O 5721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28728 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 8519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8519 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 52, 'TRANS': 1036} Chain breaks: 5 Chain: "B" Number of atoms: 8520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8520 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 5 Chain: "C" Number of atoms: 8605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8605 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 53, 'TRANS': 1045} Chain breaks: 4 Chain: "D" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.96, per 1000 atoms: 0.63 Number of scatterers: 28728 At special positions: 0 Unit cell: (150.975, 150.975, 250.8, 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 123 16.00 O 5721 8.00 N 4653 7.00 C 18231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.18 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=1.92 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.37 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 108 " distance=2.05 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 Atom "HETATM28544 O5 NAG B1403 .*. O " rejected from bonding due to valence issues. Atom "HETATM28726 O5 NAG C1408 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG h 2 " - " MAN h 3 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 3 " " NAG g 1 " - " FUC g 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 148 " " NAG A1403 " - " ASN A 234 " " NAG A1404 " - " ASN A 282 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG A1408 " - " ASN A1158 " " NAG A1409 " - " ASN A 165 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 148 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 657 " " NAG B1407 " - " ASN B 709 " " NAG B1408 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 148 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 616 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG F 1 " - " ASN A 17 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A 343 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 282 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1074 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B1134 " " NAG Y 1 " - " ASN B 343 " " NAG Z 1 " - " ASN B 165 " " NAG a 1 " - " ASN C 17 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 717 " " NAG f 1 " - " ASN C 801 " " NAG g 1 " - " ASN C1074 " " NAG h 1 " - " ASN C1098 " " NAG i 1 " - " ASN C1134 " " NAG j 1 " - " ASN C 343 " " NAG k 1 " - " ASN C 165 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.68 Conformation dependent library (CDL) restraints added in 3.5 seconds 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6550 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 48 sheets defined 25.5% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 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 349 through 353 removed outlier: 3.758A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.106A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.074A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 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: 3.910A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.670A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.778A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.149A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.898A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.560A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.151A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 3.956A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.539A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.562A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.385A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.694A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.622A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.640A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.786A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.085A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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: 4.411A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.016A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.989A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.263A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.172A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.660A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.908A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.908A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.292A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.884A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.934A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.032A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.719A pdb=" N TYR D 51 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 removed outlier: 4.450A pdb=" N GLY D 85 " --> pdb=" O GLN D 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.046A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.966A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.515A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.674A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 3.723A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.655A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.221A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 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 653 through 655 removed outlier: 3.626A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.877A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.454A 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: 5.851A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.460A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.154A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.557A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.283A 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: 3.520A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 3.794A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.175A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.627A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.806A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.072A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.010A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.330A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.780A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.477A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) 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 27 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 31 current: chain 'C' and resid 78 through 79 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 3.738A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 11.322A pdb=" N SER C 221 " --> pdb=" O PRO C 209 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.522A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.621A 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 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 120 removed outlier: 7.092A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.657A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 354 through 358 current: chain 'C' and resid 507 through 517 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.430A 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: 4.002A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.499A 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: 5.881A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.434A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AE8, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 4.213A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 23 through 25 removed outlier: 6.071A pdb=" N ALA D 35 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER D 104 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 102 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 29 through 30 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 29 through 30 current: chain 'D' and resid 64 through 71 removed outlier: 3.853A pdb=" N SER D 76 " --> pdb=" O ASN D 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 76 through 79 current: chain 'D' and resid 124 through 128 Processing sheet with id=AF2, first strand: chain 'E' and resid 25 through 26 removed outlier: 4.157A pdb=" N VAL E 39 " --> pdb=" O ILE E 95 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 30 through 33 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 30 through 33 current: chain 'E' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 64 through 68 current: chain 'E' and resid 117 through 118 No H-bonds generated for sheet with id=AF3 1019 hydrogen bonds defined for protein. 2808 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: 13.76 Time building geometry restraints manager: 8.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4879 1.31 - 1.44: 8056 1.44 - 1.57: 16268 1.57 - 1.69: 1 1.69 - 1.82: 156 Bond restraints: 29360 Sorted by residual: bond pdb=" CA PRO A 527 " pdb=" C PRO A 527 " ideal model delta sigma weight residual 1.520 1.457 0.062 1.42e-02 4.96e+03 1.91e+01 bond pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.86e+01 bond pdb=" N LEU C 84 " pdb=" CA LEU C 84 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.67e+01 bond pdb=" CA ARG C 355 " pdb=" C ARG C 355 " ideal model delta sigma weight residual 1.522 1.568 -0.046 1.14e-02 7.69e+03 1.66e+01 bond pdb=" N ILE C 233 " pdb=" CA ILE C 233 " ideal model delta sigma weight residual 1.455 1.503 -0.048 1.18e-02 7.18e+03 1.65e+01 ... (remaining 29355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 31621 2.10 - 4.19: 7678 4.19 - 6.29: 588 6.29 - 8.39: 32 8.39 - 10.49: 7 Bond angle restraints: 39926 Sorted by residual: angle pdb=" N ARG C1091 " pdb=" CA ARG C1091 " pdb=" C ARG C1091 " ideal model delta sigma weight residual 111.03 102.81 8.22 1.11e+00 8.12e-01 5.48e+01 angle pdb=" N GLY B 103 " pdb=" CA GLY B 103 " pdb=" C GLY B 103 " ideal model delta sigma weight residual 111.85 119.39 -7.54 1.06e+00 8.90e-01 5.06e+01 angle pdb=" N SER A 810 " pdb=" CA SER A 810 " pdb=" C SER A 810 " ideal model delta sigma weight residual 112.92 121.19 -8.27 1.23e+00 6.61e-01 4.52e+01 angle pdb=" N VAL B 213 " pdb=" CA VAL B 213 " pdb=" C VAL B 213 " ideal model delta sigma weight residual 110.42 116.32 -5.90 9.40e-01 1.13e+00 3.94e+01 angle pdb=" N ARG E 81 " pdb=" CA ARG E 81 " pdb=" C ARG E 81 " ideal model delta sigma weight residual 112.87 120.24 -7.37 1.20e+00 6.94e-01 3.77e+01 ... (remaining 39921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.27: 17791 24.27 - 48.54: 675 48.54 - 72.81: 188 72.81 - 97.08: 44 97.08 - 121.35: 32 Dihedral angle restraints: 18730 sinusoidal: 8541 harmonic: 10189 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -164.60 78.60 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -149.74 63.74 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -145.37 59.37 1 1.00e+01 1.00e-02 4.71e+01 ... (remaining 18727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 4767 0.340 - 0.680: 15 0.680 - 1.020: 2 1.020 - 1.359: 1 1.359 - 1.699: 2 Chirality restraints: 4787 Sorted by residual: chirality pdb=" C1 MAN N 3 " pdb=" O4 NAG N 2 " pdb=" C2 MAN N 3 " pdb=" O5 MAN N 3 " both_signs ideal model delta sigma weight residual False 2.40 1.97 0.43 2.00e-02 2.50e+03 4.56e+02 chirality pdb=" C1 MAN X 3 " pdb=" O4 NAG X 2 " pdb=" C2 MAN X 3 " pdb=" O5 MAN X 3 " both_signs ideal model delta sigma weight residual False 2.40 1.99 0.41 2.00e-02 2.50e+03 4.29e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.71e+02 ... (remaining 4784 not shown) Planarity restraints: 5082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 2 " 0.345 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG d 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG d 2 " 0.155 2.00e-02 2.50e+03 pdb=" N2 NAG d 2 " -0.525 2.00e-02 2.50e+03 pdb=" O7 NAG d 2 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " -0.333 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG d 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1407 " -0.334 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG C1407 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C1407 " -0.172 2.00e-02 2.50e+03 pdb=" N2 NAG C1407 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG C1407 " -0.079 2.00e-02 2.50e+03 ... (remaining 5079 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 48 2.48 - 3.08: 19276 3.08 - 3.69: 43416 3.69 - 4.29: 66622 4.29 - 4.90: 107837 Nonbonded interactions: 237199 Sorted by model distance: nonbonded pdb=" OE1 GLN B 14 " pdb=" NH1 ARG B 158 " model vdw 1.875 3.120 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 1.965 3.120 nonbonded pdb=" NH1 ARG B 102 " pdb=" CD2 LEU B 179 " model vdw 2.144 2.832 nonbonded pdb=" NH1 ARG A 34 " pdb=" OE2 GLU A 191 " model vdw 2.144 3.120 nonbonded pdb=" O VAL B 620 " pdb=" NH2 ARG B 634 " model vdw 2.146 3.120 ... (remaining 237194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 68 or resid 77 through 826 or resid 854 through \ 1162 or resid 1401 through 1408)) selection = (chain 'B' and (resid 14 through 623 or resid 636 through 826 or resid 854 throu \ gh 1162 or resid 1401 through 1408)) selection = (chain 'C' and (resid 14 through 68 or resid 77 through 623 or resid 636 through \ 826 or resid 854 through 1162 or resid 1401 through 1408)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'k' } ncs_group { reference = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 68.220 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 : 0.013 0.406 29501 Z= 0.826 Angle : 1.767 39.957 40303 Z= 1.148 Chirality : 0.105 1.699 4787 Planarity : 0.020 0.296 5025 Dihedral : 14.978 121.354 12051 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.79 % Favored : 93.13 % Rotamer: Outliers : 0.95 % Allowed : 6.57 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.12), residues: 3463 helix: -1.84 (0.14), residues: 766 sheet: -0.18 (0.18), residues: 721 loop : -1.79 (0.12), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.169 0.018 TRP B 104 HIS 0.010 0.002 HIS A 69 PHE 0.097 0.010 PHE A 718 TYR 0.119 0.016 TYR B 38 ARG 0.009 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.01530 ( 57) link_NAG-ASN : angle 8.58298 ( 171) link_ALPHA1-4 : bond 0.00323 ( 5) link_ALPHA1-4 : angle 2.08335 ( 15) link_BETA1-4 : bond 0.00398 ( 32) link_BETA1-4 : angle 1.17125 ( 96) hydrogen bonds : bond 0.20605 ( 1019) hydrogen bonds : angle 9.20002 ( 2808) link_BETA1-6 : bond 0.01021 ( 3) link_BETA1-6 : angle 5.34590 ( 9) SS BOND : bond 0.06057 ( 43) SS BOND : angle 3.44695 ( 86) covalent geometry : bond 0.01237 (29360) covalent geometry : angle 1.67339 (39926) Misc. bond : bond 0.40553 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 304 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.7663 (p0) cc_final: 0.7445 (p0) REVERT: B 197 ILE cc_start: 0.8635 (mm) cc_final: 0.8257 (mp) REVERT: C 32 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7538 (p90) REVERT: C 226 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.5253 (mp) REVERT: C 574 ASP cc_start: 0.6583 (t0) cc_final: 0.6248 (t0) outliers start: 29 outliers final: 9 residues processed: 327 average time/residue: 1.2676 time to fit residues: 492.4442 Evaluate side-chains 122 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain E residue 74 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 4.9990 chunk 262 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 271 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 chunk 314 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 196 ASN A 360 ASN A 540 ASN A 563 GLN A 606 ASN A 613 GLN A 853 GLN A 926 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 149 ASN B 207 HIS B 211 ASN B 448 ASN B 519 HIS B 658 ASN B 804 GLN B 913 GLN B 926 GLN B 957 GLN B 969 ASN B 978 ASN C 121 ASN C 146 HIS C 314 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 913 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 110 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.104687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.063825 restraints weight = 84958.596| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 4.32 r_work: 0.3061 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29501 Z= 0.170 Angle : 0.766 14.430 40303 Z= 0.371 Chirality : 0.047 0.409 4787 Planarity : 0.005 0.044 5025 Dihedral : 9.977 103.437 5795 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.03 % Allowed : 10.19 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 3463 helix: 0.72 (0.18), residues: 747 sheet: -0.07 (0.18), residues: 770 loop : -1.20 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 64 HIS 0.009 0.001 HIS B 519 PHE 0.025 0.002 PHE C 456 TYR 0.018 0.002 TYR A 265 ARG 0.011 0.001 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 57) link_NAG-ASN : angle 3.56702 ( 171) link_ALPHA1-4 : bond 0.02031 ( 5) link_ALPHA1-4 : angle 2.53594 ( 15) link_BETA1-4 : bond 0.00411 ( 32) link_BETA1-4 : angle 1.38923 ( 96) hydrogen bonds : bond 0.04587 ( 1019) hydrogen bonds : angle 6.48323 ( 2808) link_BETA1-6 : bond 0.01556 ( 3) link_BETA1-6 : angle 2.13868 ( 9) SS BOND : bond 0.00635 ( 43) SS BOND : angle 1.39572 ( 86) covalent geometry : bond 0.00381 (29360) covalent geometry : angle 0.72494 (39926) Misc. bond : bond 0.01134 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 126 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7350 (ptt) cc_final: 0.6547 (pmm) REVERT: A 179 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7204 (pp) REVERT: A 619 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8662 (mt-10) REVERT: A 776 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8327 (tptm) REVERT: B 174 PRO cc_start: 0.9456 (Cg_exo) cc_final: 0.9249 (Cg_endo) REVERT: B 197 ILE cc_start: 0.9165 (mm) cc_final: 0.8942 (pp) REVERT: B 455 LEU cc_start: 0.8389 (tm) cc_final: 0.7856 (pp) REVERT: B 505 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8775 (m-80) REVERT: B 1010 GLN cc_start: 0.8822 (tp-100) cc_final: 0.8577 (tm-30) REVERT: C 32 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7468 (p90) REVERT: C 226 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7092 (mp) REVERT: C 422 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8934 (p0) REVERT: C 568 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: C 574 ASP cc_start: 0.7587 (t0) cc_final: 0.7280 (t0) REVERT: C 988 GLU cc_start: 0.8356 (mp0) cc_final: 0.7954 (mp0) outliers start: 62 outliers final: 14 residues processed: 177 average time/residue: 1.0640 time to fit residues: 233.1051 Evaluate side-chains 115 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain D residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 196 optimal weight: 3.9990 chunk 320 optimal weight: 0.4980 chunk 136 optimal weight: 0.6980 chunk 147 optimal weight: 0.0040 chunk 284 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 99 ASN A 188 ASN A 360 ASN A 935 GLN A1083 HIS B 613 GLN C 146 HIS C 474 GLN C 519 HIS E 57 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.104017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.061567 restraints weight = 84012.151| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.32 r_work: 0.3010 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29501 Z= 0.128 Angle : 0.644 11.997 40303 Z= 0.312 Chirality : 0.044 0.369 4787 Planarity : 0.004 0.047 5025 Dihedral : 7.651 103.992 5778 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.06 % Allowed : 11.07 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3463 helix: 1.47 (0.19), residues: 744 sheet: 0.01 (0.18), residues: 772 loop : -0.99 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 55 HIS 0.006 0.001 HIS C 519 PHE 0.028 0.001 PHE C 456 TYR 0.037 0.001 TYR A 453 ARG 0.011 0.001 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 57) link_NAG-ASN : angle 2.93426 ( 171) link_ALPHA1-4 : bond 0.01682 ( 5) link_ALPHA1-4 : angle 2.57396 ( 15) link_BETA1-4 : bond 0.00386 ( 32) link_BETA1-4 : angle 1.23017 ( 96) hydrogen bonds : bond 0.03905 ( 1019) hydrogen bonds : angle 5.97303 ( 2808) link_BETA1-6 : bond 0.01561 ( 3) link_BETA1-6 : angle 2.18958 ( 9) SS BOND : bond 0.00259 ( 43) SS BOND : angle 1.25650 ( 86) covalent geometry : bond 0.00282 (29360) covalent geometry : angle 0.60944 (39926) Misc. bond : bond 0.00167 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 112 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7478 (ptt) cc_final: 0.6660 (pmm) REVERT: A 179 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7287 (pp) REVERT: A 368 LEU cc_start: 0.9319 (mt) cc_final: 0.8976 (tp) REVERT: A 390 LEU cc_start: 0.9166 (mt) cc_final: 0.8883 (mp) REVERT: A 619 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8607 (mt-10) REVERT: A 776 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8272 (tptm) REVERT: B 174 PRO cc_start: 0.9487 (Cg_exo) cc_final: 0.9281 (Cg_endo) REVERT: B 197 ILE cc_start: 0.9156 (mm) cc_final: 0.8932 (pp) REVERT: B 455 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7907 (pp) REVERT: B 505 TYR cc_start: 0.9137 (t80) cc_final: 0.8422 (t80) REVERT: C 32 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7576 (p90) REVERT: C 226 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7241 (mt) REVERT: C 360 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.9021 (t0) REVERT: C 408 ARG cc_start: 0.8780 (ttp80) cc_final: 0.8422 (ppt90) REVERT: C 489 TYR cc_start: 0.8461 (m-80) cc_final: 0.8095 (m-80) REVERT: C 988 GLU cc_start: 0.8332 (mp0) cc_final: 0.7751 (mp0) REVERT: D 53 MET cc_start: 0.4407 (mmm) cc_final: 0.3716 (tmm) outliers start: 63 outliers final: 15 residues processed: 161 average time/residue: 0.9939 time to fit residues: 201.6186 Evaluate side-chains 110 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 187 optimal weight: 2.9990 chunk 321 optimal weight: 1.9990 chunk 267 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 307 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 121 ASN A 360 ASN A1002 GLN B 856 ASN B 901 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 394 ASN C 460 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.100797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058474 restraints weight = 82240.248| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 4.12 r_work: 0.2868 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 29501 Z= 0.223 Angle : 0.660 11.551 40303 Z= 0.319 Chirality : 0.045 0.361 4787 Planarity : 0.004 0.049 5025 Dihedral : 6.781 96.401 5778 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.35 % Allowed : 11.40 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3463 helix: 1.68 (0.19), residues: 745 sheet: -0.12 (0.18), residues: 786 loop : -0.91 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 128 HIS 0.008 0.001 HIS A1064 PHE 0.018 0.002 PHE C 898 TYR 0.025 0.002 TYR C 453 ARG 0.008 0.001 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 57) link_NAG-ASN : angle 2.74090 ( 171) link_ALPHA1-4 : bond 0.02011 ( 5) link_ALPHA1-4 : angle 2.68829 ( 15) link_BETA1-4 : bond 0.00343 ( 32) link_BETA1-4 : angle 1.35080 ( 96) hydrogen bonds : bond 0.03924 ( 1019) hydrogen bonds : angle 5.90756 ( 2808) link_BETA1-6 : bond 0.01683 ( 3) link_BETA1-6 : angle 2.44478 ( 9) SS BOND : bond 0.00312 ( 43) SS BOND : angle 1.30705 ( 86) covalent geometry : bond 0.00511 (29360) covalent geometry : angle 0.62913 (39926) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 93 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7044 (OUTLIER) cc_final: 0.6759 (t0) REVERT: A 177 MET cc_start: 0.7634 (ptt) cc_final: 0.7185 (pmm) REVERT: A 179 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7690 (pp) REVERT: A 309 GLU cc_start: 0.8612 (pm20) cc_final: 0.8374 (pm20) REVERT: A 619 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8643 (mt-10) REVERT: A 994 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8337 (t0) REVERT: B 455 LEU cc_start: 0.8503 (tm) cc_final: 0.7993 (pp) REVERT: C 32 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7511 (p90) REVERT: C 214 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7736 (ppp80) REVERT: C 226 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7635 (mt) REVERT: C 408 ARG cc_start: 0.8813 (ttp80) cc_final: 0.8314 (ppt90) REVERT: C 422 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8816 (p0) REVERT: C 489 TYR cc_start: 0.8374 (m-80) cc_final: 0.8160 (m-80) REVERT: C 988 GLU cc_start: 0.8773 (mp0) cc_final: 0.8214 (mp0) REVERT: D 53 MET cc_start: 0.4380 (mmm) cc_final: 0.3782 (tmt) outliers start: 72 outliers final: 29 residues processed: 158 average time/residue: 1.1067 time to fit residues: 214.8576 Evaluate side-chains 116 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 324 optimal weight: 3.9990 chunk 306 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 338 optimal weight: 10.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN B 675 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 460 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.100287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.058632 restraints weight = 80878.058| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.17 r_work: 0.2839 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 29501 Z= 0.226 Angle : 0.642 16.063 40303 Z= 0.307 Chirality : 0.044 0.413 4787 Planarity : 0.004 0.048 5025 Dihedral : 6.379 94.167 5778 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.96 % Allowed : 12.48 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3463 helix: 1.79 (0.19), residues: 739 sheet: -0.21 (0.17), residues: 800 loop : -0.91 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 64 HIS 0.007 0.001 HIS A1064 PHE 0.015 0.001 PHE C 456 TYR 0.022 0.001 TYR C1067 ARG 0.006 0.000 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 57) link_NAG-ASN : angle 2.63854 ( 171) link_ALPHA1-4 : bond 0.01856 ( 5) link_ALPHA1-4 : angle 2.72442 ( 15) link_BETA1-4 : bond 0.00404 ( 32) link_BETA1-4 : angle 1.27686 ( 96) hydrogen bonds : bond 0.03817 ( 1019) hydrogen bonds : angle 5.83809 ( 2808) link_BETA1-6 : bond 0.01558 ( 3) link_BETA1-6 : angle 2.43678 ( 9) SS BOND : bond 0.00306 ( 43) SS BOND : angle 1.22162 ( 86) covalent geometry : bond 0.00519 (29360) covalent geometry : angle 0.61241 (39926) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 86 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7681 (pp) REVERT: A 309 GLU cc_start: 0.8585 (pm20) cc_final: 0.8345 (pm20) REVERT: A 619 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8635 (mt-10) REVERT: A 994 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8386 (t0) REVERT: B 455 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7990 (pp) REVERT: B 986 LYS cc_start: 0.9302 (tppp) cc_final: 0.8681 (tptt) REVERT: C 32 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7491 (p90) REVERT: C 177 MET cc_start: 0.6192 (ptm) cc_final: 0.5429 (pmm) REVERT: C 408 ARG cc_start: 0.8822 (ttp80) cc_final: 0.8341 (ppt90) REVERT: C 489 TYR cc_start: 0.8552 (m-80) cc_final: 0.8316 (m-80) REVERT: C 988 GLU cc_start: 0.8862 (mp0) cc_final: 0.8361 (mp0) REVERT: D 53 MET cc_start: 0.4575 (mmm) cc_final: 0.3842 (tmt) outliers start: 60 outliers final: 24 residues processed: 141 average time/residue: 1.0782 time to fit residues: 189.1972 Evaluate side-chains 104 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 155 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 260 optimal weight: 9.9990 chunk 230 optimal weight: 10.0000 chunk 228 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 300 optimal weight: 0.2980 chunk 114 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 762 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.099923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.055646 restraints weight = 81070.242| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.11 r_work: 0.2840 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29501 Z= 0.206 Angle : 0.619 10.395 40303 Z= 0.297 Chirality : 0.043 0.319 4787 Planarity : 0.003 0.049 5025 Dihedral : 5.847 88.875 5776 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 2.03 % Allowed : 12.61 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3463 helix: 1.93 (0.19), residues: 734 sheet: -0.28 (0.17), residues: 811 loop : -0.87 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 64 HIS 0.006 0.001 HIS A1064 PHE 0.014 0.001 PHE C 898 TYR 0.021 0.001 TYR C1067 ARG 0.005 0.000 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 57) link_NAG-ASN : angle 2.46634 ( 171) link_ALPHA1-4 : bond 0.02052 ( 5) link_ALPHA1-4 : angle 3.06982 ( 15) link_BETA1-4 : bond 0.00323 ( 32) link_BETA1-4 : angle 1.20182 ( 96) hydrogen bonds : bond 0.03661 ( 1019) hydrogen bonds : angle 5.73139 ( 2808) link_BETA1-6 : bond 0.01831 ( 3) link_BETA1-6 : angle 2.55766 ( 9) SS BOND : bond 0.00295 ( 43) SS BOND : angle 1.13327 ( 86) covalent geometry : bond 0.00469 (29360) covalent geometry : angle 0.59071 (39926) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 93 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8469 (t60) cc_final: 0.8031 (t60) REVERT: A 177 MET cc_start: 0.7739 (pmm) cc_final: 0.7406 (pmt) REVERT: A 179 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7852 (pp) REVERT: A 309 GLU cc_start: 0.8520 (pm20) cc_final: 0.8281 (pm20) REVERT: A 619 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8698 (mt-10) REVERT: A 994 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8361 (t0) REVERT: B 455 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.7943 (pp) REVERT: B 986 LYS cc_start: 0.9296 (tppp) cc_final: 0.8790 (tptt) REVERT: C 32 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7429 (p90) REVERT: C 408 ARG cc_start: 0.8776 (ttp80) cc_final: 0.8302 (ppt90) REVERT: C 489 TYR cc_start: 0.8636 (m-80) cc_final: 0.8406 (m-80) REVERT: C 988 GLU cc_start: 0.9001 (mp0) cc_final: 0.8557 (mp0) REVERT: D 53 MET cc_start: 0.4508 (mmm) cc_final: 0.3667 (tmt) outliers start: 62 outliers final: 26 residues processed: 148 average time/residue: 1.0749 time to fit residues: 196.9191 Evaluate side-chains 112 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 225 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 45 optimal weight: 50.0000 chunk 188 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 253 optimal weight: 9.9990 chunk 275 optimal weight: 0.6980 chunk 199 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 762 GLN B1010 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.100461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056898 restraints weight = 81017.957| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.03 r_work: 0.2869 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29501 Z= 0.136 Angle : 0.584 9.754 40303 Z= 0.278 Chirality : 0.042 0.328 4787 Planarity : 0.003 0.050 5025 Dihedral : 5.375 81.883 5776 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 1.73 % Allowed : 13.30 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3463 helix: 2.11 (0.19), residues: 720 sheet: -0.30 (0.17), residues: 822 loop : -0.78 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS B1064 PHE 0.022 0.001 PHE C 456 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 57) link_NAG-ASN : angle 2.32028 ( 171) link_ALPHA1-4 : bond 0.01937 ( 5) link_ALPHA1-4 : angle 3.10037 ( 15) link_BETA1-4 : bond 0.00365 ( 32) link_BETA1-4 : angle 1.13187 ( 96) hydrogen bonds : bond 0.03397 ( 1019) hydrogen bonds : angle 5.61224 ( 2808) link_BETA1-6 : bond 0.01957 ( 3) link_BETA1-6 : angle 2.54514 ( 9) SS BOND : bond 0.00229 ( 43) SS BOND : angle 0.92702 ( 86) covalent geometry : bond 0.00306 (29360) covalent geometry : angle 0.55810 (39926) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 87 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8322 (t60) cc_final: 0.7975 (t60) REVERT: A 177 MET cc_start: 0.7866 (pmm) cc_final: 0.7424 (pmt) REVERT: A 179 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7481 (pp) REVERT: A 309 GLU cc_start: 0.8482 (pm20) cc_final: 0.8193 (pm20) REVERT: A 994 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8332 (t0) REVERT: B 455 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7879 (pp) REVERT: B 565 PHE cc_start: 0.7892 (m-80) cc_final: 0.7630 (m-80) REVERT: B 986 LYS cc_start: 0.9288 (tppp) cc_final: 0.8815 (tptt) REVERT: C 32 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7294 (p90) REVERT: C 177 MET cc_start: 0.6249 (ptm) cc_final: 0.5347 (pmm) REVERT: C 408 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8317 (ppt90) REVERT: C 988 GLU cc_start: 0.8959 (mp0) cc_final: 0.8498 (mp0) REVERT: C 1002 GLN cc_start: 0.9069 (tp40) cc_final: 0.8762 (tp40) REVERT: D 53 MET cc_start: 0.4482 (mmm) cc_final: 0.3637 (tmt) outliers start: 53 outliers final: 26 residues processed: 136 average time/residue: 1.0853 time to fit residues: 185.3767 Evaluate side-chains 108 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 91 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 172 optimal weight: 0.0970 chunk 136 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 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 = 0.3940 r_free = 0.3940 target = 0.099862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058680 restraints weight = 80492.618| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.82 r_work: 0.2840 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 29501 Z= 0.222 Angle : 0.625 9.905 40303 Z= 0.299 Chirality : 0.043 0.311 4787 Planarity : 0.004 0.050 5025 Dihedral : 5.201 68.441 5776 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 1.67 % Allowed : 13.69 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3463 helix: 1.98 (0.19), residues: 738 sheet: -0.39 (0.17), residues: 795 loop : -0.79 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.008 0.001 HIS A1064 PHE 0.016 0.001 PHE C 898 TYR 0.025 0.001 TYR A 453 ARG 0.006 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 57) link_NAG-ASN : angle 2.37495 ( 171) link_ALPHA1-4 : bond 0.01951 ( 5) link_ALPHA1-4 : angle 3.30929 ( 15) link_BETA1-4 : bond 0.00286 ( 32) link_BETA1-4 : angle 1.21964 ( 96) hydrogen bonds : bond 0.03719 ( 1019) hydrogen bonds : angle 5.70831 ( 2808) link_BETA1-6 : bond 0.01757 ( 3) link_BETA1-6 : angle 2.41420 ( 9) SS BOND : bond 0.00306 ( 43) SS BOND : angle 1.08304 ( 86) covalent geometry : bond 0.00510 (29360) covalent geometry : angle 0.59877 (39926) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 87 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8629 (t60) cc_final: 0.8220 (t60) REVERT: A 177 MET cc_start: 0.7931 (pmm) cc_final: 0.7538 (pmt) REVERT: A 179 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8007 (pp) REVERT: A 309 GLU cc_start: 0.8583 (pm20) cc_final: 0.8306 (pm20) REVERT: A 994 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8344 (t0) REVERT: B 455 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8020 (pp) REVERT: B 565 PHE cc_start: 0.7923 (m-80) cc_final: 0.7679 (m-80) REVERT: B 986 LYS cc_start: 0.9304 (tppp) cc_final: 0.8819 (tptt) REVERT: C 115 GLN cc_start: 0.9143 (mt0) cc_final: 0.8697 (mm-40) REVERT: C 408 ARG cc_start: 0.8842 (ttp80) cc_final: 0.8383 (ppt90) REVERT: C 988 GLU cc_start: 0.9003 (mp0) cc_final: 0.8593 (mp0) REVERT: C 1002 GLN cc_start: 0.9115 (tp40) cc_final: 0.8871 (tp40) REVERT: C 1141 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9006 (tm) REVERT: D 53 MET cc_start: 0.4308 (mmm) cc_final: 0.3964 (tmt) outliers start: 51 outliers final: 28 residues processed: 132 average time/residue: 1.1610 time to fit residues: 188.3196 Evaluate side-chains 110 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 222 optimal weight: 0.0570 chunk 193 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 184 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 235 optimal weight: 9.9990 chunk 252 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** 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 = 0.3961 r_free = 0.3961 target = 0.100629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.058562 restraints weight = 80228.973| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 4.20 r_work: 0.2863 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29501 Z= 0.119 Angle : 0.584 11.444 40303 Z= 0.278 Chirality : 0.042 0.311 4787 Planarity : 0.003 0.050 5025 Dihedral : 4.909 58.351 5776 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 1.40 % Allowed : 14.18 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3463 helix: 2.18 (0.19), residues: 720 sheet: -0.32 (0.17), residues: 823 loop : -0.73 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS C1048 PHE 0.040 0.001 PHE C 456 TYR 0.019 0.001 TYR C1067 ARG 0.003 0.000 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 57) link_NAG-ASN : angle 2.20453 ( 171) link_ALPHA1-4 : bond 0.01879 ( 5) link_ALPHA1-4 : angle 3.11734 ( 15) link_BETA1-4 : bond 0.00374 ( 32) link_BETA1-4 : angle 1.11037 ( 96) hydrogen bonds : bond 0.03324 ( 1019) hydrogen bonds : angle 5.53008 ( 2808) link_BETA1-6 : bond 0.01912 ( 3) link_BETA1-6 : angle 2.30861 ( 9) SS BOND : bond 0.00226 ( 43) SS BOND : angle 0.90706 ( 86) covalent geometry : bond 0.00264 (29360) covalent geometry : angle 0.55991 (39926) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8565 (t60) cc_final: 0.7751 (t60) REVERT: A 177 MET cc_start: 0.7920 (pmm) cc_final: 0.7449 (pmt) REVERT: A 179 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7722 (pp) REVERT: A 214 ARG cc_start: 0.7668 (tpm170) cc_final: 0.7279 (tpm170) REVERT: A 309 GLU cc_start: 0.8485 (pm20) cc_final: 0.8180 (pm20) REVERT: A 988 GLU cc_start: 0.8988 (pt0) cc_final: 0.8524 (pm20) REVERT: B 455 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7884 (pp) REVERT: B 565 PHE cc_start: 0.7856 (m-80) cc_final: 0.7562 (m-80) REVERT: B 986 LYS cc_start: 0.9275 (tppp) cc_final: 0.8824 (tptt) REVERT: C 115 GLN cc_start: 0.9173 (mt0) cc_final: 0.8567 (mm-40) REVERT: C 177 MET cc_start: 0.6293 (ptm) cc_final: 0.5353 (pmm) REVERT: C 408 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8315 (ppt90) REVERT: C 988 GLU cc_start: 0.9029 (mp0) cc_final: 0.8604 (mp0) REVERT: C 1002 GLN cc_start: 0.9095 (tp40) cc_final: 0.8835 (tp40) REVERT: D 53 MET cc_start: 0.4414 (mmm) cc_final: 0.3576 (tmt) outliers start: 43 outliers final: 29 residues processed: 125 average time/residue: 1.2532 time to fit residues: 188.9292 Evaluate side-chains 112 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 64 optimal weight: 1.9990 chunk 307 optimal weight: 0.9980 chunk 288 optimal weight: 4.9990 chunk 265 optimal weight: 0.6980 chunk 325 optimal weight: 50.0000 chunk 254 optimal weight: 0.0570 chunk 93 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 194 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 474 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.100883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.058963 restraints weight = 80550.515| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 4.00 r_work: 0.2880 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29501 Z= 0.116 Angle : 0.574 9.543 40303 Z= 0.273 Chirality : 0.042 0.310 4787 Planarity : 0.003 0.055 5025 Dihedral : 4.666 58.425 5776 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.14 % Allowed : 14.44 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3463 helix: 2.25 (0.19), residues: 720 sheet: -0.25 (0.17), residues: 823 loop : -0.70 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 258 HIS 0.003 0.001 HIS A1048 PHE 0.017 0.001 PHE A 855 TYR 0.018 0.001 TYR C1067 ARG 0.014 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 57) link_NAG-ASN : angle 2.15816 ( 171) link_ALPHA1-4 : bond 0.01880 ( 5) link_ALPHA1-4 : angle 3.13708 ( 15) link_BETA1-4 : bond 0.00344 ( 32) link_BETA1-4 : angle 1.10283 ( 96) hydrogen bonds : bond 0.03248 ( 1019) hydrogen bonds : angle 5.43039 ( 2808) link_BETA1-6 : bond 0.01950 ( 3) link_BETA1-6 : angle 2.24912 ( 9) SS BOND : bond 0.00204 ( 43) SS BOND : angle 0.89729 ( 86) covalent geometry : bond 0.00259 (29360) covalent geometry : angle 0.55055 (39926) Misc. bond : bond 0.00005 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8615 (t60) cc_final: 0.7928 (t60) REVERT: A 153 MET cc_start: 0.8379 (pmt) cc_final: 0.7858 (pmm) REVERT: A 177 MET cc_start: 0.7945 (pmm) cc_final: 0.7158 (pmt) REVERT: A 179 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7697 (pp) REVERT: A 214 ARG cc_start: 0.7614 (tpm170) cc_final: 0.7282 (tpm170) REVERT: A 309 GLU cc_start: 0.8477 (pm20) cc_final: 0.8188 (pm20) REVERT: A 368 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8890 (tp) REVERT: A 988 GLU cc_start: 0.8970 (pt0) cc_final: 0.8528 (pm20) REVERT: B 408 ARG cc_start: 0.8762 (mmp80) cc_final: 0.8559 (pmt-80) REVERT: B 455 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7930 (pp) REVERT: B 565 PHE cc_start: 0.7873 (m-80) cc_final: 0.7578 (m-80) REVERT: B 986 LYS cc_start: 0.9280 (tppp) cc_final: 0.8855 (tptt) REVERT: C 115 GLN cc_start: 0.9134 (mt0) cc_final: 0.8565 (mm-40) REVERT: C 177 MET cc_start: 0.6300 (ptm) cc_final: 0.5326 (pmm) REVERT: C 988 GLU cc_start: 0.8982 (mp0) cc_final: 0.8546 (mp0) REVERT: C 1002 GLN cc_start: 0.9060 (tp40) cc_final: 0.8810 (tp40) REVERT: D 53 MET cc_start: 0.4366 (mmm) cc_final: 0.3790 (tmt) REVERT: D 70 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.5649 (mp) outliers start: 35 outliers final: 24 residues processed: 119 average time/residue: 1.3481 time to fit residues: 192.5885 Evaluate side-chains 108 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 35 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 291 optimal weight: 0.0770 chunk 123 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** 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 = 0.3949 r_free = 0.3949 target = 0.100070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.056302 restraints weight = 80564.223| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.31 r_work: 0.2839 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29501 Z= 0.180 Angle : 0.598 9.699 40303 Z= 0.285 Chirality : 0.043 0.310 4787 Planarity : 0.003 0.050 5025 Dihedral : 4.670 57.913 5775 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 1.05 % Allowed : 14.73 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.14), residues: 3463 helix: 2.24 (0.19), residues: 719 sheet: -0.30 (0.17), residues: 824 loop : -0.73 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 64 HIS 0.005 0.001 HIS A1064 PHE 0.041 0.001 PHE C 456 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 57) link_NAG-ASN : angle 2.20432 ( 171) link_ALPHA1-4 : bond 0.01890 ( 5) link_ALPHA1-4 : angle 3.15611 ( 15) link_BETA1-4 : bond 0.00309 ( 32) link_BETA1-4 : angle 1.15041 ( 96) hydrogen bonds : bond 0.03451 ( 1019) hydrogen bonds : angle 5.49989 ( 2808) link_BETA1-6 : bond 0.01953 ( 3) link_BETA1-6 : angle 2.11871 ( 9) SS BOND : bond 0.00263 ( 43) SS BOND : angle 0.95751 ( 86) covalent geometry : bond 0.00413 (29360) covalent geometry : angle 0.57427 (39926) Misc. bond : bond 0.00002 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22981.11 seconds wall clock time: 396 minutes 30.27 seconds (23790.27 seconds total)