Starting phenix.real_space_refine on Tue Jun 24 02:05:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d56_27206/06_2025/8d56_27206_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d56_27206/06_2025/8d56_27206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d56_27206/06_2025/8d56_27206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d56_27206/06_2025/8d56_27206.map" model { file = "/net/cci-nas-00/data/ceres_data/8d56_27206/06_2025/8d56_27206_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d56_27206/06_2025/8d56_27206_neut.cif" } resolution = 3.0 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= 0.012 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 119 5.16 5 C 17602 2.51 5 N 4474 2.21 5 O 5479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27674 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8715 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 51, 'TRANS': 1058} Chain breaks: 4 Chain: "B" Number of atoms: 8820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1124, 8820 Classifications: {'peptide': 1124} Link IDs: {'PTRANS': 51, 'TRANS': 1072} Chain breaks: 3 Chain: "C" Number of atoms: 8777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8777 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 51, 'TRANS': 1067} Chain breaks: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 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: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 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: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 18.12, per 1000 atoms: 0.65 Number of scatterers: 27674 At special positions: 0 Unit cell: (147.74, 143.59, 219.12, 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 119 16.00 O 5479 8.00 N 4474 7.00 C 17602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=1.98 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 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=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=1.99 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG G 2 " - " MAN G 3 " " NAG I 2 " - " MAN I 3 " " NAG J 2 " - " MAN J 3 " " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG Q 2 " - " MAN Q 3 " " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG V 2 " - " MAN V 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG f 2 " - " MAN f 3 " " NAG g 2 " - " MAN g 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG K 1 " - " FUC K 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 3 " " NAG e 1 " - " FUC e 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 331 " " NAG A1403 " - " ASN A 343 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 331 " " NAG B1403 " - " ASN B 343 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 331 " " NAG C1403 " - " ASN C 343 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 122 " " NAG O 1 " - " ASN B 165 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 616 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1074 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 122 " " NAG Y 1 " - " ASN C 165 " " NAG Z 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 282 " " NAG b 1 " - " ASN C 616 " " NAG c 1 " - " ASN C 717 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C1074 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 7.47 Conformation dependent library (CDL) restraints added in 3.2 seconds 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6284 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 44 sheets defined 27.0% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 96 through 99 removed outlier: 3.820A pdb=" N ASN A 99 " --> pdb=" O GLU A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 99' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.797A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.534A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.360A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.081A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.628A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.734A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.767A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.041A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.590A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.212A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.551A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.564A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.051A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.375A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.555A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.695A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.606A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.663A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.536A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.341A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.673A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.662A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 4.335A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.736A pdb=" N ASN C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 100' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 405 through 411 removed outlier: 5.026A pdb=" N SER C 408 " --> pdb=" O ASN 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: 3.606A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 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: 3.912A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.205A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.629A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 848 Processing helix chain 'C' and resid 848 through 855 removed outlier: 4.086A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.713A 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: 4.114A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.557A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.182A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.652A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.004A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.430A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 31 removed outlier: 8.347A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.025A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.621A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.902A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.764A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 327 removed outlier: 4.211A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.654A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.995A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.545A 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 728 removed outlier: 6.689A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.689A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.272A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.339A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.117A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.421A 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: 3.654A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.076A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.766A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.524A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.253A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.158A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 357 removed outlier: 4.015A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.747A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.765A pdb=" N TYR B 453 " --> pdb=" O ARG B 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.585A 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: 6.684A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.051A 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 removed outlier: 6.495A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.495A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.317A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.151A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 20 through 31 removed outlier: 3.613A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS C 69 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY C 261 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.569A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.361A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE2, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.971A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, 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=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.026A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3102 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: 13.47 Time building geometry restraints manager: 9.02 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: 4679 1.31 - 1.44: 7827 1.44 - 1.57: 15637 1.57 - 1.70: 4 1.70 - 1.82: 149 Bond restraints: 28296 Sorted by residual: bond pdb=" N PHE B 133 " pdb=" CA PHE B 133 " ideal model delta sigma weight residual 1.454 1.394 0.061 1.17e-02 7.31e+03 2.67e+01 bond pdb=" CA PHE B 65 " pdb=" C PHE B 65 " ideal model delta sigma weight residual 1.526 1.465 0.061 1.36e-02 5.41e+03 2.00e+01 bond pdb=" CA ARG C 466 " pdb=" C ARG C 466 " ideal model delta sigma weight residual 1.521 1.569 -0.048 1.20e-02 6.94e+03 1.59e+01 bond pdb=" CA HIS B 207 " pdb=" C HIS B 207 " ideal model delta sigma weight residual 1.522 1.569 -0.047 1.18e-02 7.18e+03 1.56e+01 bond pdb=" C GLN C 607 " pdb=" O GLN C 607 " ideal model delta sigma weight residual 1.234 1.190 0.044 1.17e-02 7.31e+03 1.40e+01 ... (remaining 28291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 32162 2.38 - 4.76: 5884 4.76 - 7.14: 397 7.14 - 9.52: 32 9.52 - 11.90: 8 Bond angle restraints: 38483 Sorted by residual: angle pdb=" N SER C 172 " pdb=" CA SER C 172 " pdb=" C SER C 172 " ideal model delta sigma weight residual 108.45 119.22 -10.77 1.26e+00 6.30e-01 7.31e+01 angle pdb=" C LEU B 216 " pdb=" CA LEU B 216 " pdb=" CB LEU B 216 " ideal model delta sigma weight residual 111.20 116.42 -5.22 7.10e-01 1.98e+00 5.41e+01 angle pdb=" N ARG C 246 " pdb=" CA ARG C 246 " pdb=" C ARG C 246 " ideal model delta sigma weight residual 112.25 102.33 9.92 1.36e+00 5.41e-01 5.32e+01 angle pdb=" N ASN A 125 " pdb=" CA ASN A 125 " pdb=" C ASN A 125 " ideal model delta sigma weight residual 108.32 120.22 -11.90 1.64e+00 3.72e-01 5.26e+01 angle pdb=" N ASN C 125 " pdb=" CA ASN C 125 " pdb=" C ASN C 125 " ideal model delta sigma weight residual 108.45 117.51 -9.06 1.26e+00 6.30e-01 5.17e+01 ... (remaining 38478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 17108 24.76 - 49.52: 746 49.52 - 74.29: 181 74.29 - 99.05: 57 99.05 - 123.81: 41 Dihedral angle restraints: 18133 sinusoidal: 8354 harmonic: 9779 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -164.88 78.88 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 166.32 -73.32 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" CA PRO C 491 " pdb=" C PRO C 491 " pdb=" N LEU C 492 " pdb=" CA LEU C 492 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 18130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.257: 4563 0.257 - 0.514: 65 0.514 - 0.771: 6 0.771 - 1.028: 0 1.028 - 1.284: 3 Chirality restraints: 4637 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.70e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.68e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.44e+01 ... (remaining 4634 not shown) Planarity restraints: 4872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1402 " 0.208 2.00e-02 2.50e+03 1.73e-01 3.74e+02 pdb=" C7 NAG B1402 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1402 " 0.149 2.00e-02 2.50e+03 pdb=" N2 NAG B1402 " -0.283 2.00e-02 2.50e+03 pdb=" O7 NAG B1402 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 104 " 0.211 2.00e-02 2.50e+03 1.08e-01 2.92e+02 pdb=" CG TRP B 104 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 104 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP B 104 " -0.099 2.00e-02 2.50e+03 pdb=" NE1 TRP B 104 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP B 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 104 " -0.144 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 104 " 0.131 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 104 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP B 104 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1407 " 0.158 2.00e-02 2.50e+03 1.32e-01 2.18e+02 pdb=" C7 NAG B1407 " -0.041 2.00e-02 2.50e+03 pdb=" C8 NAG B1407 " 0.115 2.00e-02 2.50e+03 pdb=" N2 NAG B1407 " -0.218 2.00e-02 2.50e+03 pdb=" O7 NAG B1407 " -0.014 2.00e-02 2.50e+03 ... (remaining 4869 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 3 2.15 - 2.83: 7600 2.83 - 3.52: 37587 3.52 - 4.21: 65331 4.21 - 4.90: 110578 Nonbonded interactions: 221099 Sorted by model distance: nonbonded pdb=" ND2 ASN C 334 " pdb=" O ASN C 360 " model vdw 1.457 3.120 nonbonded pdb=" CD1 LEU B 452 " pdb=" O ARG B 493 " model vdw 1.606 3.460 nonbonded pdb=" O SER B 112 " pdb=" OE2 GLU B 132 " model vdw 2.048 3.040 nonbonded pdb=" O SER C 98 " pdb=" NH2 ARG C 102 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR C 453 " pdb=" NH1 ARG C 493 " model vdw 2.217 3.120 ... (remaining 221094 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 624 or resid 629 through 1160 or resid 1401 thr \ ough 1407)) selection = (chain 'B' and (resid 14 through 71 or resid 80 through 248 or resid 257 through \ 624 or resid 629 through 835 or resid 848 through 1160 or resid 1401 through 14 \ 07)) selection = (chain 'C' and (resid 14 through 248 or resid 257 through 835 or resid 848 throu \ gh 1160 or resid 1401 through 1407)) } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.050 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: 0.040 Extract box with map and model: 1.240 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 67.480 Find NCS groups from input model: 2.520 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: 0.010 Load rotamer database and sin/cos tables:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.012 0.061 28442 Z= 0.737 Angle : 1.777 22.906 38877 Z= 1.153 Chirality : 0.105 1.284 4637 Planarity : 0.013 0.173 4821 Dihedral : 16.187 123.809 11717 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.63 % Favored : 92.25 % Rotamer: Outliers : 2.60 % Allowed : 8.32 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.13), residues: 3327 helix: -1.36 (0.16), residues: 752 sheet: -0.00 (0.20), residues: 615 loop : -1.86 (0.12), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.211 0.026 TRP B 104 HIS 0.017 0.002 HIS C 69 PHE 0.076 0.010 PHE B 718 TYR 0.119 0.016 TYR A1138 ARG 0.010 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.02349 ( 51) link_NAG-ASN : angle 6.32611 ( 153) link_ALPHA1-4 : bond 0.00671 ( 18) link_ALPHA1-4 : angle 2.17633 ( 54) link_BETA1-4 : bond 0.00502 ( 30) link_BETA1-4 : angle 1.73867 ( 90) hydrogen bonds : bond 0.18469 ( 1086) hydrogen bonds : angle 8.69994 ( 3102) link_BETA1-6 : bond 0.01014 ( 3) link_BETA1-6 : angle 1.96667 ( 9) SS BOND : bond 0.01365 ( 44) SS BOND : angle 2.42009 ( 88) covalent geometry : bond 0.01205 (28296) covalent geometry : angle 1.73270 (38483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 238 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7641 (tt) REVERT: A 365 TYR cc_start: 0.7559 (p90) cc_final: 0.6942 (m-80) REVERT: A 468 ILE cc_start: 0.8327 (pt) cc_final: 0.7705 (mm) REVERT: A 739 THR cc_start: 0.8111 (m) cc_final: 0.7846 (p) REVERT: B 54 LEU cc_start: 0.9269 (mt) cc_final: 0.9051 (mt) REVERT: B 489 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: C 201 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.4572 (t80) REVERT: C 366 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8741 (p) REVERT: C 375 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6528 (p90) outliers start: 76 outliers final: 17 residues processed: 299 average time/residue: 1.3606 time to fit residues: 480.0125 Evaluate side-chains 125 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 491 PRO Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 0.8980 chunk 253 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 261 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 474 GLN A 487 ASN A 913 GLN A 955 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN A1106 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 188 ASN B 245 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 450 ASN B 506 GLN B 613 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN B1010 GLN B1071 GLN B1159 HIS C 14 GLN C 69 HIS C 196 ASN C 245 HIS C 607 GLN C1002 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.098256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059816 restraints weight = 73531.618| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.68 r_work: 0.2875 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28442 Z= 0.163 Angle : 0.784 13.001 38877 Z= 0.383 Chirality : 0.047 0.309 4637 Planarity : 0.004 0.059 4821 Dihedral : 12.811 111.650 5745 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.67 % Allowed : 11.88 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3327 helix: 0.94 (0.19), residues: 746 sheet: 0.12 (0.18), residues: 718 loop : -1.44 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 152 HIS 0.009 0.001 HIS C1048 PHE 0.018 0.002 PHE A 106 TYR 0.022 0.002 TYR C1067 ARG 0.009 0.001 ARG C 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 51) link_NAG-ASN : angle 3.11981 ( 153) link_ALPHA1-4 : bond 0.01446 ( 18) link_ALPHA1-4 : angle 2.64973 ( 54) link_BETA1-4 : bond 0.00452 ( 30) link_BETA1-4 : angle 1.50348 ( 90) hydrogen bonds : bond 0.04976 ( 1086) hydrogen bonds : angle 6.36815 ( 3102) link_BETA1-6 : bond 0.01541 ( 3) link_BETA1-6 : angle 1.71373 ( 9) SS BOND : bond 0.00424 ( 44) SS BOND : angle 1.42152 ( 88) covalent geometry : bond 0.00357 (28296) covalent geometry : angle 0.74925 (38483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 120 time to evaluate : 2.824 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 212 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8314 (tp) REVERT: A 269 TYR cc_start: 0.8422 (m-80) cc_final: 0.7907 (m-80) REVERT: A 365 TYR cc_start: 0.7559 (p90) cc_final: 0.6516 (m-80) REVERT: A 452 LEU cc_start: 0.9074 (tp) cc_final: 0.8788 (tm) REVERT: A 468 ILE cc_start: 0.8095 (pt) cc_final: 0.7842 (mt) REVERT: A 633 TRP cc_start: 0.8076 (OUTLIER) cc_final: 0.7440 (p-90) REVERT: B 245 HIS cc_start: 0.6863 (OUTLIER) cc_final: 0.6597 (p90) REVERT: B 364 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8191 (t0) REVERT: B 429 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6822 (p90) REVERT: B 456 PHE cc_start: 0.8461 (m-80) cc_final: 0.7671 (m-10) REVERT: B 489 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: B 523 THR cc_start: 0.8617 (p) cc_final: 0.8224 (t) REVERT: B 1146 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7913 (p0) REVERT: C 14 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7197 (pp30) REVERT: C 69 HIS cc_start: 0.5621 (OUTLIER) cc_final: 0.4957 (p-80) REVERT: C 170 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: C 342 PHE cc_start: 0.7467 (m-80) cc_final: 0.7234 (m-10) REVERT: C 369 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7579 (p90) REVERT: C 375 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7951 (p90) REVERT: C 515 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8712 (p90) REVERT: C 658 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7738 (p0) REVERT: C 957 GLN cc_start: 0.8147 (tt0) cc_final: 0.7675 (tm-30) REVERT: C 1029 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9163 (tpp) outliers start: 78 outliers final: 18 residues processed: 187 average time/residue: 0.9910 time to fit residues: 230.9880 Evaluate side-chains 131 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 174 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 247 optimal weight: 0.0040 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 267 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.097476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058850 restraints weight = 73553.191| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.65 r_work: 0.2855 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28442 Z= 0.150 Angle : 0.708 17.040 38877 Z= 0.335 Chirality : 0.045 0.282 4637 Planarity : 0.004 0.041 4821 Dihedral : 11.254 107.999 5724 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.36 % Allowed : 13.49 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.14), residues: 3327 helix: 1.47 (0.19), residues: 754 sheet: 0.12 (0.18), residues: 728 loop : -1.34 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 152 HIS 0.009 0.001 HIS B 245 PHE 0.024 0.001 PHE C 140 TYR 0.025 0.001 TYR A 369 ARG 0.008 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 51) link_NAG-ASN : angle 2.68916 ( 153) link_ALPHA1-4 : bond 0.01604 ( 18) link_ALPHA1-4 : angle 2.64999 ( 54) link_BETA1-4 : bond 0.00333 ( 30) link_BETA1-4 : angle 1.44561 ( 90) hydrogen bonds : bond 0.04364 ( 1086) hydrogen bonds : angle 5.86501 ( 3102) link_BETA1-6 : bond 0.01619 ( 3) link_BETA1-6 : angle 2.03322 ( 9) SS BOND : bond 0.00287 ( 44) SS BOND : angle 1.26114 ( 88) covalent geometry : bond 0.00336 (28296) covalent geometry : angle 0.67661 (38483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 103 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8454 (m-80) cc_final: 0.7941 (m-80) REVERT: A 452 LEU cc_start: 0.9005 (tp) cc_final: 0.8793 (tp) REVERT: A 468 ILE cc_start: 0.8120 (pt) cc_final: 0.7884 (mt) REVERT: A 988 GLU cc_start: 0.8590 (mp0) cc_final: 0.8328 (mp0) REVERT: B 173 GLN cc_start: 0.5877 (OUTLIER) cc_final: 0.5321 (tm-30) REVERT: B 375 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.7293 (p90) REVERT: B 429 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.6793 (p90) REVERT: B 646 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8458 (mpp80) REVERT: B 985 ASP cc_start: 0.7369 (p0) cc_final: 0.6694 (p0) REVERT: C 375 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.8069 (p90) REVERT: C 658 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.7897 (p0) REVERT: C 957 GLN cc_start: 0.8214 (tt0) cc_final: 0.7730 (tm-30) outliers start: 69 outliers final: 22 residues processed: 165 average time/residue: 1.0058 time to fit residues: 208.1940 Evaluate side-chains 121 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 156 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 297 optimal weight: 2.9990 chunk 326 optimal weight: 0.6980 chunk 291 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 14 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.096893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.058036 restraints weight = 74379.048| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.67 r_work: 0.2837 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28442 Z= 0.156 Angle : 0.683 16.869 38877 Z= 0.321 Chirality : 0.044 0.249 4637 Planarity : 0.004 0.043 4821 Dihedral : 10.155 106.240 5718 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.71 % Allowed : 13.70 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3327 helix: 1.81 (0.20), residues: 740 sheet: 0.14 (0.18), residues: 763 loop : -1.26 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.005 0.001 HIS C 69 PHE 0.019 0.001 PHE A 338 TYR 0.021 0.001 TYR C1067 ARG 0.006 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 51) link_NAG-ASN : angle 2.48926 ( 153) link_ALPHA1-4 : bond 0.01643 ( 18) link_ALPHA1-4 : angle 3.10602 ( 54) link_BETA1-4 : bond 0.00301 ( 30) link_BETA1-4 : angle 1.42354 ( 90) hydrogen bonds : bond 0.04084 ( 1086) hydrogen bonds : angle 5.64648 ( 3102) link_BETA1-6 : bond 0.01753 ( 3) link_BETA1-6 : angle 2.06347 ( 9) SS BOND : bond 0.00256 ( 44) SS BOND : angle 1.31815 ( 88) covalent geometry : bond 0.00355 (28296) covalent geometry : angle 0.65021 (38483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 100 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8453 (m-80) cc_final: 0.7944 (m-80) REVERT: A 468 ILE cc_start: 0.8175 (pt) cc_final: 0.7902 (mt) REVERT: A 988 GLU cc_start: 0.8625 (mp0) cc_final: 0.8361 (mp0) REVERT: B 173 GLN cc_start: 0.6104 (OUTLIER) cc_final: 0.5536 (tm-30) REVERT: B 465 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: B 634 ARG cc_start: 0.7032 (ttp80) cc_final: 0.6595 (ttp80) REVERT: B 646 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8415 (mpp80) REVERT: C 269 TYR cc_start: 0.7367 (m-10) cc_final: 0.7055 (m-80) REVERT: C 371 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6142 (p90) REVERT: C 375 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7703 (p90) REVERT: C 658 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8049 (p0) REVERT: C 849 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8203 (tt) outliers start: 79 outliers final: 30 residues processed: 169 average time/residue: 1.0127 time to fit residues: 214.6434 Evaluate side-chains 125 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 102 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 216 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 239 GLN B 314 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 506 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 69 HIS C 580 GLN C 914 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.095944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056943 restraints weight = 73804.271| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.66 r_work: 0.2805 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28442 Z= 0.179 Angle : 0.680 18.251 38877 Z= 0.318 Chirality : 0.044 0.234 4637 Planarity : 0.004 0.043 4821 Dihedral : 9.252 104.930 5718 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.08 % Allowed : 14.01 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3327 helix: 1.92 (0.20), residues: 739 sheet: 0.25 (0.18), residues: 724 loop : -1.16 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.007 0.001 HIS B1064 PHE 0.017 0.001 PHE C 338 TYR 0.024 0.001 TYR B 170 ARG 0.006 0.001 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 51) link_NAG-ASN : angle 2.38202 ( 153) link_ALPHA1-4 : bond 0.01724 ( 18) link_ALPHA1-4 : angle 2.96133 ( 54) link_BETA1-4 : bond 0.00240 ( 30) link_BETA1-4 : angle 1.44056 ( 90) hydrogen bonds : bond 0.04029 ( 1086) hydrogen bonds : angle 5.53683 ( 3102) link_BETA1-6 : bond 0.01795 ( 3) link_BETA1-6 : angle 1.99759 ( 9) SS BOND : bond 0.00267 ( 44) SS BOND : angle 1.23878 ( 88) covalent geometry : bond 0.00411 (28296) covalent geometry : angle 0.65067 (38483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 100 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: A 988 GLU cc_start: 0.8649 (mp0) cc_final: 0.8400 (mp0) REVERT: B 173 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5735 (tm-30) REVERT: B 429 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6454 (p90) REVERT: B 465 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: B 634 ARG cc_start: 0.6961 (ttp80) cc_final: 0.6493 (ttp80) REVERT: B 646 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8445 (mpp80) REVERT: B 990 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8253 (tm-30) REVERT: B 1050 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.8534 (ppp) REVERT: B 1146 ASP cc_start: 0.8784 (m-30) cc_final: 0.8168 (p0) REVERT: C 269 TYR cc_start: 0.7370 (m-10) cc_final: 0.6938 (m-80) REVERT: C 368 LEU cc_start: 0.9174 (tt) cc_final: 0.8899 (tt) REVERT: C 371 PHE cc_start: 0.6799 (OUTLIER) cc_final: 0.6036 (p90) REVERT: C 375 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7760 (p90) REVERT: C 658 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8426 (p0) REVERT: C 830 ASP cc_start: 0.7312 (t0) cc_final: 0.7054 (t0) REVERT: C 849 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8239 (tt) REVERT: C 912 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.9010 (p) outliers start: 90 outliers final: 42 residues processed: 178 average time/residue: 0.9821 time to fit residues: 220.5303 Evaluate side-chains 144 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 91 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 275 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 294 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 311 optimal weight: 0.9980 chunk 270 optimal weight: 5.9990 chunk 263 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 133 optimal weight: 0.0050 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 677 GLN B 955 ASN C 69 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.096225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.057369 restraints weight = 73958.333| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.65 r_work: 0.2822 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28442 Z= 0.145 Angle : 0.657 17.990 38877 Z= 0.305 Chirality : 0.044 0.237 4637 Planarity : 0.003 0.041 4821 Dihedral : 8.729 103.848 5715 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.64 % Allowed : 15.00 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3327 helix: 2.01 (0.20), residues: 738 sheet: 0.32 (0.18), residues: 727 loop : -1.15 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 104 HIS 0.018 0.001 HIS C 69 PHE 0.028 0.001 PHE B 168 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 51) link_NAG-ASN : angle 2.31277 ( 153) link_ALPHA1-4 : bond 0.01741 ( 18) link_ALPHA1-4 : angle 2.89028 ( 54) link_BETA1-4 : bond 0.00291 ( 30) link_BETA1-4 : angle 1.37826 ( 90) hydrogen bonds : bond 0.03809 ( 1086) hydrogen bonds : angle 5.42398 ( 3102) link_BETA1-6 : bond 0.01774 ( 3) link_BETA1-6 : angle 2.00213 ( 9) SS BOND : bond 0.00277 ( 44) SS BOND : angle 1.29640 ( 88) covalent geometry : bond 0.00327 (28296) covalent geometry : angle 0.62709 (38483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 91 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: A 988 GLU cc_start: 0.8654 (mp0) cc_final: 0.8407 (mp0) REVERT: A 1148 PHE cc_start: 0.5463 (OUTLIER) cc_final: 0.5237 (t80) REVERT: B 173 GLN cc_start: 0.6341 (OUTLIER) cc_final: 0.5823 (tm-30) REVERT: B 429 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.6500 (p90) REVERT: B 634 ARG cc_start: 0.6899 (ttp80) cc_final: 0.6466 (ttp80) REVERT: B 646 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8456 (mpp80) REVERT: B 1050 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8419 (ppp) REVERT: B 1146 ASP cc_start: 0.8815 (m-30) cc_final: 0.8204 (p0) REVERT: C 69 HIS cc_start: 0.5523 (OUTLIER) cc_final: 0.4787 (p-80) REVERT: C 242 LEU cc_start: 0.8420 (tp) cc_final: 0.8166 (tm) REVERT: C 269 TYR cc_start: 0.7414 (m-10) cc_final: 0.6591 (m-80) REVERT: C 271 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.9075 (pm20) REVERT: C 368 LEU cc_start: 0.9168 (tt) cc_final: 0.8909 (tt) REVERT: C 371 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.6134 (p90) REVERT: C 375 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7766 (p90) REVERT: C 658 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8476 (p0) REVERT: C 830 ASP cc_start: 0.7287 (t0) cc_final: 0.7033 (t0) REVERT: C 849 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8256 (tt) outliers start: 77 outliers final: 38 residues processed: 161 average time/residue: 0.9407 time to fit residues: 191.6873 Evaluate side-chains 142 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 1 optimal weight: 7.9990 chunk 208 optimal weight: 0.6980 chunk 309 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 328 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN C 69 HIS ** C1054 GLN ** 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 = 0.3830 r_free = 0.3830 target = 0.095660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.056677 restraints weight = 74112.695| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.66 r_work: 0.2801 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28442 Z= 0.182 Angle : 0.667 18.259 38877 Z= 0.310 Chirality : 0.044 0.231 4637 Planarity : 0.004 0.040 4821 Dihedral : 8.394 103.222 5714 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.84 % Allowed : 14.79 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3327 helix: 2.00 (0.20), residues: 738 sheet: 0.31 (0.18), residues: 719 loop : -1.15 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.027 0.001 HIS C 69 PHE 0.024 0.001 PHE B 168 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 51) link_NAG-ASN : angle 2.33223 ( 153) link_ALPHA1-4 : bond 0.01696 ( 18) link_ALPHA1-4 : angle 2.86549 ( 54) link_BETA1-4 : bond 0.00245 ( 30) link_BETA1-4 : angle 1.41137 ( 90) hydrogen bonds : bond 0.03912 ( 1086) hydrogen bonds : angle 5.42832 ( 3102) link_BETA1-6 : bond 0.01720 ( 3) link_BETA1-6 : angle 2.00813 ( 9) SS BOND : bond 0.00304 ( 44) SS BOND : angle 1.49226 ( 88) covalent geometry : bond 0.00420 (28296) covalent geometry : angle 0.63651 (38483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 92 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: A 988 GLU cc_start: 0.8636 (mp0) cc_final: 0.8397 (mp0) REVERT: B 173 GLN cc_start: 0.6484 (OUTLIER) cc_final: 0.5977 (tm-30) REVERT: B 429 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.6447 (p90) REVERT: B 634 ARG cc_start: 0.6850 (ttp80) cc_final: 0.6380 (ttp80) REVERT: B 646 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8478 (mpp80) REVERT: B 1050 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8419 (ppp) REVERT: B 1146 ASP cc_start: 0.8838 (m-30) cc_final: 0.8232 (p0) REVERT: C 69 HIS cc_start: 0.5651 (OUTLIER) cc_final: 0.5175 (p-80) REVERT: C 242 LEU cc_start: 0.8459 (tp) cc_final: 0.8215 (tm) REVERT: C 269 TYR cc_start: 0.7412 (m-10) cc_final: 0.6669 (m-80) REVERT: C 271 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.9106 (pm20) REVERT: C 309 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8424 (mp0) REVERT: C 368 LEU cc_start: 0.9179 (tt) cc_final: 0.8932 (tt) REVERT: C 371 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6009 (p90) REVERT: C 375 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7797 (p90) REVERT: C 658 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8616 (p0) REVERT: C 830 ASP cc_start: 0.7299 (t0) cc_final: 0.7055 (t0) REVERT: C 849 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8237 (tt) outliers start: 83 outliers final: 47 residues processed: 165 average time/residue: 0.9895 time to fit residues: 205.1596 Evaluate side-chains 145 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 87 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 178 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 288 optimal weight: 0.7980 chunk 188 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 69 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.095029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.055966 restraints weight = 74284.082| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.68 r_work: 0.2784 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28442 Z= 0.213 Angle : 0.675 18.637 38877 Z= 0.315 Chirality : 0.044 0.228 4637 Planarity : 0.004 0.040 4821 Dihedral : 8.203 102.782 5714 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 2.47 % Allowed : 15.10 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3327 helix: 1.98 (0.19), residues: 738 sheet: 0.28 (0.18), residues: 724 loop : -1.16 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.025 0.001 HIS C 69 PHE 0.026 0.001 PHE A 855 TYR 0.020 0.001 TYR C1067 ARG 0.005 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 51) link_NAG-ASN : angle 2.35926 ( 153) link_ALPHA1-4 : bond 0.01633 ( 18) link_ALPHA1-4 : angle 2.87162 ( 54) link_BETA1-4 : bond 0.00224 ( 30) link_BETA1-4 : angle 1.42999 ( 90) hydrogen bonds : bond 0.04034 ( 1086) hydrogen bonds : angle 5.44791 ( 3102) link_BETA1-6 : bond 0.01771 ( 3) link_BETA1-6 : angle 1.94998 ( 9) SS BOND : bond 0.00285 ( 44) SS BOND : angle 1.41514 ( 88) covalent geometry : bond 0.00496 (28296) covalent geometry : angle 0.64554 (38483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 89 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: A 988 GLU cc_start: 0.8637 (mp0) cc_final: 0.8414 (mp0) REVERT: B 173 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.6049 (tm-30) REVERT: B 429 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.6552 (p90) REVERT: B 646 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8493 (mpp80) REVERT: B 990 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8097 (pp20) REVERT: B 1050 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8438 (ppp) REVERT: B 1146 ASP cc_start: 0.8876 (m-30) cc_final: 0.8269 (p0) REVERT: C 242 LEU cc_start: 0.8449 (tp) cc_final: 0.8227 (tm) REVERT: C 269 TYR cc_start: 0.7316 (m-10) cc_final: 0.6547 (m-80) REVERT: C 271 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9075 (pm20) REVERT: C 309 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8438 (mp0) REVERT: C 371 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.6110 (p90) REVERT: C 375 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7777 (p90) REVERT: C 658 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8839 (p0) REVERT: C 661 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8741 (mp0) REVERT: C 849 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8210 (tt) REVERT: C 912 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.9025 (p) REVERT: C 1148 PHE cc_start: 0.5310 (t80) cc_final: 0.5106 (t80) outliers start: 72 outliers final: 46 residues processed: 153 average time/residue: 1.2840 time to fit residues: 248.1054 Evaluate side-chains 143 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 86 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 255 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 295 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 260 optimal weight: 0.5980 chunk 291 optimal weight: 0.7980 chunk 150 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 955 ASN C 69 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.096214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.057379 restraints weight = 73864.330| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.68 r_work: 0.2824 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28442 Z= 0.123 Angle : 0.639 19.438 38877 Z= 0.297 Chirality : 0.043 0.232 4637 Planarity : 0.003 0.040 4821 Dihedral : 7.942 101.654 5714 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 1.95 % Allowed : 15.92 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3327 helix: 2.13 (0.20), residues: 736 sheet: 0.35 (0.19), residues: 707 loop : -1.09 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 104 HIS 0.022 0.001 HIS C 69 PHE 0.031 0.001 PHE A 855 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 51) link_NAG-ASN : angle 2.23063 ( 153) link_ALPHA1-4 : bond 0.01591 ( 18) link_ALPHA1-4 : angle 2.80541 ( 54) link_BETA1-4 : bond 0.00320 ( 30) link_BETA1-4 : angle 1.33410 ( 90) hydrogen bonds : bond 0.03631 ( 1086) hydrogen bonds : angle 5.29762 ( 3102) link_BETA1-6 : bond 0.01938 ( 3) link_BETA1-6 : angle 1.90073 ( 9) SS BOND : bond 0.00240 ( 44) SS BOND : angle 1.21035 ( 88) covalent geometry : bond 0.00270 (28296) covalent geometry : angle 0.61074 (38483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 95 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7138 (mm-30) REVERT: A 988 GLU cc_start: 0.8671 (mp0) cc_final: 0.8441 (mp0) REVERT: B 173 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6026 (tm-30) REVERT: B 429 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.6399 (p90) REVERT: B 634 ARG cc_start: 0.6782 (ttp80) cc_final: 0.6335 (ttp80) REVERT: B 646 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8456 (mpp80) REVERT: B 1050 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8299 (ppp) REVERT: B 1146 ASP cc_start: 0.8853 (m-30) cc_final: 0.8249 (p0) REVERT: C 69 HIS cc_start: 0.5748 (OUTLIER) cc_final: 0.5373 (p-80) REVERT: C 242 LEU cc_start: 0.8403 (tp) cc_final: 0.8188 (tm) REVERT: C 269 TYR cc_start: 0.7298 (m-10) cc_final: 0.6379 (m-80) REVERT: C 271 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.9085 (pm20) REVERT: C 371 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.6190 (p90) REVERT: C 375 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7794 (p90) REVERT: C 658 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8619 (p0) REVERT: C 661 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8715 (mp0) REVERT: C 849 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8202 (tt) REVERT: C 912 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8998 (p) outliers start: 57 outliers final: 39 residues processed: 149 average time/residue: 1.0046 time to fit residues: 190.9778 Evaluate side-chains 137 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 86 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 912 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 172 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 chunk 289 optimal weight: 0.6980 chunk 126 optimal weight: 0.0970 chunk 332 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 326 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 955 ASN C 69 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.096468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057639 restraints weight = 73838.843| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.68 r_work: 0.2832 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28442 Z= 0.120 Angle : 0.641 19.296 38877 Z= 0.298 Chirality : 0.043 0.231 4637 Planarity : 0.003 0.040 4821 Dihedral : 7.747 100.739 5712 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 1.82 % Allowed : 16.20 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3327 helix: 2.18 (0.20), residues: 736 sheet: 0.42 (0.19), residues: 690 loop : -1.05 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 104 HIS 0.012 0.001 HIS C 69 PHE 0.029 0.001 PHE B 823 TYR 0.039 0.001 TYR A 144 ARG 0.004 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 51) link_NAG-ASN : angle 2.20064 ( 153) link_ALPHA1-4 : bond 0.01569 ( 18) link_ALPHA1-4 : angle 2.78224 ( 54) link_BETA1-4 : bond 0.00310 ( 30) link_BETA1-4 : angle 1.31417 ( 90) hydrogen bonds : bond 0.03539 ( 1086) hydrogen bonds : angle 5.23666 ( 3102) link_BETA1-6 : bond 0.01963 ( 3) link_BETA1-6 : angle 1.68431 ( 9) SS BOND : bond 0.00234 ( 44) SS BOND : angle 1.16751 ( 88) covalent geometry : bond 0.00263 (28296) covalent geometry : angle 0.61377 (38483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6654 Ramachandran restraints generated. 3327 Oldfield, 0 Emsley, 3327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 89 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: A 988 GLU cc_start: 0.8670 (mp0) cc_final: 0.8441 (mp0) REVERT: B 173 GLN cc_start: 0.6705 (OUTLIER) cc_final: 0.6009 (tm-30) REVERT: B 429 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.6529 (p90) REVERT: B 634 ARG cc_start: 0.6716 (ttp80) cc_final: 0.6291 (ttp80) REVERT: B 646 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8470 (mpp80) REVERT: B 990 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8042 (pp20) REVERT: B 1050 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.8266 (ppp) REVERT: B 1146 ASP cc_start: 0.8869 (m-30) cc_final: 0.8243 (p0) REVERT: C 69 HIS cc_start: 0.5921 (OUTLIER) cc_final: 0.5386 (p-80) REVERT: C 269 TYR cc_start: 0.7343 (m-10) cc_final: 0.6724 (m-80) REVERT: C 271 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.9083 (pm20) REVERT: C 371 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6187 (p90) REVERT: C 375 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7773 (p90) REVERT: C 658 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8572 (p0) REVERT: C 661 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8714 (mp0) REVERT: C 849 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8218 (tt) REVERT: C 912 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.9001 (p) outliers start: 53 outliers final: 40 residues processed: 138 average time/residue: 0.9765 time to fit residues: 169.6465 Evaluate side-chains 136 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 84 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 912 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 38 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 276 optimal weight: 0.0870 chunk 137 optimal weight: 0.9990 chunk 212 optimal weight: 0.4980 chunk 270 optimal weight: 6.9990 chunk 289 optimal weight: 0.8980 chunk 266 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 613 GLN C 69 HIS C 957 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.096545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.057819 restraints weight = 74090.437| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.65 r_work: 0.2837 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28442 Z= 0.121 Angle : 0.634 19.028 38877 Z= 0.294 Chirality : 0.043 0.230 4637 Planarity : 0.003 0.041 4821 Dihedral : 7.590 99.783 5712 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 2.12 % Allowed : 15.89 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3327 helix: 2.24 (0.20), residues: 731 sheet: 0.39 (0.19), residues: 708 loop : -1.02 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 104 HIS 0.018 0.001 HIS C 69 PHE 0.028 0.001 PHE B 823 TYR 0.026 0.001 TYR A 144 ARG 0.004 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 51) link_NAG-ASN : angle 2.18223 ( 153) link_ALPHA1-4 : bond 0.01536 ( 18) link_ALPHA1-4 : angle 2.76163 ( 54) link_BETA1-4 : bond 0.00310 ( 30) link_BETA1-4 : angle 1.29723 ( 90) hydrogen bonds : bond 0.03492 ( 1086) hydrogen bonds : angle 5.20244 ( 3102) link_BETA1-6 : bond 0.01819 ( 3) link_BETA1-6 : angle 1.41659 ( 9) SS BOND : bond 0.00226 ( 44) SS BOND : angle 1.13970 ( 88) covalent geometry : bond 0.00265 (28296) covalent geometry : angle 0.60723 (38483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18304.72 seconds wall clock time: 321 minutes 25.03 seconds (19285.03 seconds total)