Starting phenix.real_space_refine on Fri Feb 6 20:06:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n1t_24122/02_2026/7n1t_24122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n1t_24122/02_2026/7n1t_24122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n1t_24122/02_2026/7n1t_24122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n1t_24122/02_2026/7n1t_24122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n1t_24122/02_2026/7n1t_24122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n1t_24122/02_2026/7n1t_24122.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.044 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 120 5.16 5 C 17592 2.51 5 N 4467 2.21 5 O 5538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27717 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8732 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 53, 'TRANS': 1061} Chain breaks: 3 Chain: "B" Number of atoms: 8732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8732 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 53, 'TRANS': 1061} Chain breaks: 3 Chain: "C" Number of atoms: 8732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8732 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 53, 'TRANS': 1061} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 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: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.52, per 1000 atoms: 0.24 Number of scatterers: 27717 At special positions: 0 Unit cell: (148.512, 145.212, 195.541, 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 120 16.00 O 5538 8.00 N 4467 7.00 C 17592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 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=2.02 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=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 E 2 " - " MAN E 3 " " NAG G 2 " - " MAN G 3 " " NAG H 2 " - " MAN H 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG 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 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG h 1 " - " FUC h 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " NAG A1404 " - " ASN A 343 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG A1408 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 343 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 657 " " NAG B1407 " - " ASN B 709 " " NAG B1408 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 17 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6258 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 49 sheets defined 27.8% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.777A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.191A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.159A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.722A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 618 through 623 removed outlier: 4.169A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 removed outlier: 4.223A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.584A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.885A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.456A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.991A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 847 removed outlier: 3.960A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.171A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.677A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.509A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.931A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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: 3.921A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1160 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.714A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.894A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.860A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.508A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.893A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.524A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 847 removed outlier: 4.412A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 removed outlier: 4.066A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.557A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.608A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.724A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.620A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.326A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 987 through 1033 removed outlier: 4.098A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 3.916A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.857A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.385A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (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 616 through 620 removed outlier: 3.820A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.907A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.911A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.560A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.717A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 847 Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.685A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.503A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 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: 4.257A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.312A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 3.755A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.728A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.048A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.048A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.487A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.770A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ARG A 246 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 101 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.614A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.939A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N HIS A 245 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 141 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.475A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.963A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.628A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.715A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.760A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.487A pdb=" N VAL A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.244A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.759A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.290A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.696A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.671A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.082A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.943A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.670A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.769A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.872A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.885A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.321A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.814A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.676A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.170A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.746A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.077A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.311A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.043A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.637A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.939A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.120A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, 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: 6.812A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, 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: 6.812A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.232A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.465A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3111 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: 7.46 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4392 1.29 - 1.42: 7553 1.42 - 1.56: 16231 1.56 - 1.69: 6 1.69 - 1.82: 150 Bond restraints: 28332 Sorted by residual: bond pdb=" C ARG A 237 " pdb=" O ARG A 237 " ideal model delta sigma weight residual 1.234 1.159 0.075 1.22e-02 6.72e+03 3.80e+01 bond pdb=" C ARG C 237 " pdb=" O ARG C 237 " ideal model delta sigma weight residual 1.234 1.159 0.075 1.29e-02 6.01e+03 3.37e+01 bond pdb=" C ARG B 995 " pdb=" O ARG B 995 " ideal model delta sigma weight residual 1.236 1.168 0.067 1.17e-02 7.31e+03 3.32e+01 bond pdb=" C ARG A1014 " pdb=" O ARG A1014 " ideal model delta sigma weight residual 1.236 1.173 0.063 1.19e-02 7.06e+03 2.78e+01 bond pdb=" C ARG B 815 " pdb=" O ARG B 815 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.23e-02 6.61e+03 2.22e+01 ... (remaining 28327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 32049 2.45 - 4.90: 6075 4.90 - 7.35: 383 7.35 - 9.80: 32 9.80 - 12.25: 2 Bond angle restraints: 38541 Sorted by residual: angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 108.24 120.49 -12.25 1.32e+00 5.74e-01 8.61e+01 angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 108.24 119.99 -11.75 1.32e+00 5.74e-01 7.92e+01 angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 111.82 102.11 9.71 1.16e+00 7.43e-01 7.00e+01 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 119.92 -7.32 1.00e+00 1.00e+00 5.36e+01 angle pdb=" N PRO B 25 " pdb=" CA PRO B 25 " pdb=" C PRO B 25 " ideal model delta sigma weight residual 110.70 118.44 -7.74 1.22e+00 6.72e-01 4.02e+01 ... (remaining 38536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.42: 17437 25.42 - 50.83: 623 50.83 - 76.25: 169 76.25 - 101.67: 34 101.67 - 127.08: 64 Dihedral angle restraints: 18327 sinusoidal: 8583 harmonic: 9744 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 169.90 -76.90 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual -86.00 -149.72 63.72 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual -86.00 -149.05 63.05 1 1.00e+01 1.00e-02 5.25e+01 ... (remaining 18324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.254: 4594 0.254 - 0.508: 77 0.508 - 0.762: 4 0.762 - 1.016: 2 1.016 - 1.270: 2 Chirality restraints: 4679 Sorted by residual: 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 -2.57 0.17 2.00e-02 2.50e+03 6.83e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.40e+01 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.14e+01 ... (remaining 4676 not shown) Planarity restraints: 4883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " 0.133 2.00e-02 2.50e+03 1.71e-01 3.67e+02 pdb=" CG ASN C1134 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " -0.288 2.00e-02 2.50e+03 pdb=" C1 NAG j 1 " 0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.144 2.00e-02 2.50e+03 1.61e-01 3.25e+02 pdb=" CG ASN B 331 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.257 2.00e-02 2.50e+03 pdb=" C1 NAG B1403 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.139 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" CG ASN A 61 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.240 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " 0.174 2.00e-02 2.50e+03 ... (remaining 4880 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 36 2.51 - 3.11: 19369 3.11 - 3.71: 40774 3.71 - 4.30: 60952 4.30 - 4.90: 98900 Nonbonded interactions: 220031 Sorted by model distance: nonbonded pdb=" NH1 ARG A 403 " pdb=" OE1 GLU A 406 " model vdw 1.917 3.120 nonbonded pdb=" CG2 VAL C 16 " pdb=" NH1 ARG C 158 " model vdw 1.997 3.540 nonbonded pdb=" O PHE A 559 " pdb=" NH2 ARG A 577 " model vdw 2.119 3.120 nonbonded pdb=" O ILE B 742 " pdb=" NH1 ARG B1000 " model vdw 2.134 3.120 nonbonded pdb=" NH1 ARG B 905 " pdb=" O LEU B1049 " model vdw 2.233 3.120 ... (remaining 220026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'Z' selection = chain 'b' selection = chain 'e' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain '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 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 27.510 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.439 28490 Z= 0.817 Angle : 1.871 36.918 38970 Z= 1.187 Chirality : 0.109 1.270 4679 Planarity : 0.012 0.126 4827 Dihedral : 16.474 127.083 11934 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.96 % Favored : 93.32 % Rotamer: Outliers : 0.96 % Allowed : 3.98 % Favored : 95.06 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 3321 helix: -0.93 (0.17), residues: 717 sheet: 0.04 (0.19), residues: 651 loop : -1.60 (0.12), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 357 TYR 0.115 0.018 TYR C1138 PHE 0.087 0.013 PHE A 133 TRP 0.131 0.022 TRP A 104 HIS 0.014 0.004 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.01433 (28332) covalent geometry : angle 1.80029 (38541) SS BOND : bond 0.01150 ( 45) SS BOND : angle 2.18982 ( 90) hydrogen bonds : bond 0.16524 ( 1114) hydrogen bonds : angle 8.67598 ( 3111) link_ALPHA1-4 : bond 0.02589 ( 21) link_ALPHA1-4 : angle 3.34518 ( 63) link_BETA1-4 : bond 0.02223 ( 33) link_BETA1-4 : angle 3.80451 ( 99) link_BETA1-6 : bond 0.03275 ( 3) link_BETA1-6 : angle 2.92334 ( 9) link_NAG-ASN : bond 0.08712 ( 56) link_NAG-ASN : angle 7.25995 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 653 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8803 (mm) cc_final: 0.8550 (mp) REVERT: A 113 LYS cc_start: 0.7754 (tptt) cc_final: 0.6951 (tppt) REVERT: A 121 ASN cc_start: 0.6327 (OUTLIER) cc_final: 0.5829 (t0) REVERT: A 191 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7155 (mt-10) REVERT: A 207 HIS cc_start: 0.7483 (m170) cc_final: 0.6642 (m170) REVERT: A 314 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 319 ARG cc_start: 0.8248 (ptp-170) cc_final: 0.8047 (ptp90) REVERT: A 401 VAL cc_start: 0.8878 (t) cc_final: 0.8614 (m) REVERT: A 428 ASP cc_start: 0.8361 (p0) cc_final: 0.8157 (p0) REVERT: A 453 TYR cc_start: 0.7310 (p90) cc_final: 0.6637 (p90) REVERT: A 468 ILE cc_start: 0.8066 (mm) cc_final: 0.7459 (mm) REVERT: A 524 VAL cc_start: 0.8255 (p) cc_final: 0.7954 (p) REVERT: A 539 VAL cc_start: 0.9125 (m) cc_final: 0.8764 (t) REVERT: A 558 LYS cc_start: 0.8730 (mptt) cc_final: 0.8445 (mmtm) REVERT: A 564 GLN cc_start: 0.8150 (tp40) cc_final: 0.7766 (tp40) REVERT: A 571 ASP cc_start: 0.7862 (t0) cc_final: 0.7586 (t70) REVERT: A 574 ASP cc_start: 0.8100 (t70) cc_final: 0.7763 (t0) REVERT: A 633 TRP cc_start: 0.8691 (p-90) cc_final: 0.8456 (p-90) REVERT: A 735 SER cc_start: 0.8942 (t) cc_final: 0.8253 (p) REVERT: A 780 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 804 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7319 (mm-40) REVERT: A 820 ASP cc_start: 0.8373 (m-30) cc_final: 0.8107 (m-30) REVERT: A 855 PHE cc_start: 0.8798 (m-10) cc_final: 0.8488 (m-80) REVERT: A 933 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8397 (mtmm) REVERT: A 935 GLN cc_start: 0.8295 (tt0) cc_final: 0.7539 (tt0) REVERT: A 950 ASP cc_start: 0.7919 (t0) cc_final: 0.7625 (t0) REVERT: A 979 ASP cc_start: 0.7803 (t0) cc_final: 0.7424 (t0) REVERT: A 988 GLU cc_start: 0.7836 (pm20) cc_final: 0.7608 (pm20) REVERT: A 994 ASP cc_start: 0.8007 (t70) cc_final: 0.7699 (t0) REVERT: A 1002 GLN cc_start: 0.7749 (tp40) cc_final: 0.7471 (mm-40) REVERT: A 1072 GLU cc_start: 0.8354 (pm20) cc_final: 0.8086 (pm20) REVERT: A 1092 GLU cc_start: 0.7229 (pm20) cc_final: 0.6926 (pm20) REVERT: B 52 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 113 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7798 (mmmm) REVERT: B 128 ILE cc_start: 0.8350 (mt) cc_final: 0.8143 (mp) REVERT: B 140 PHE cc_start: 0.7829 (p90) cc_final: 0.7495 (p90) REVERT: B 314 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7316 (tm-30) REVERT: B 422 ASN cc_start: 0.7944 (p0) cc_final: 0.7661 (p0) REVERT: B 453 TYR cc_start: 0.7626 (p90) cc_final: 0.6879 (p90) REVERT: B 524 VAL cc_start: 0.8033 (p) cc_final: 0.7705 (p) REVERT: B 735 SER cc_start: 0.8532 (t) cc_final: 0.8016 (p) REVERT: B 765 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7774 (ttp-170) REVERT: B 790 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7361 (mtpp) REVERT: B 796 ASP cc_start: 0.7882 (t0) cc_final: 0.7642 (t0) REVERT: B 823 PHE cc_start: 0.7876 (m-80) cc_final: 0.7245 (m-80) REVERT: B 867 ASP cc_start: 0.8224 (m-30) cc_final: 0.7779 (m-30) REVERT: B 913 GLN cc_start: 0.8725 (pt0) cc_final: 0.8454 (pt0) REVERT: B 918 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7332 (mt-10) REVERT: B 921 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8192 (tttp) REVERT: B 979 ASP cc_start: 0.7811 (t0) cc_final: 0.7479 (t0) REVERT: B 1072 GLU cc_start: 0.8323 (pm20) cc_final: 0.8098 (pm20) REVERT: B 1073 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8400 (mtpp) REVERT: B 1123 SER cc_start: 0.9019 (t) cc_final: 0.8714 (t) REVERT: C 52 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8272 (tm-30) REVERT: C 54 LEU cc_start: 0.9077 (mt) cc_final: 0.8509 (mt) REVERT: C 100 ILE cc_start: 0.9089 (mp) cc_final: 0.8836 (mp) REVERT: C 129 LYS cc_start: 0.8144 (tttt) cc_final: 0.7813 (ttmm) REVERT: C 155 SER cc_start: 0.8109 (t) cc_final: 0.7365 (t) REVERT: C 188 ASN cc_start: 0.8374 (t0) cc_final: 0.8117 (t0) REVERT: C 314 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7534 (tm-30) REVERT: C 354 ASN cc_start: 0.8502 (t0) cc_final: 0.8256 (t0) REVERT: C 418 ILE cc_start: 0.9023 (mm) cc_final: 0.8770 (mt) REVERT: C 458 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8342 (mmmt) REVERT: C 549 THR cc_start: 0.8562 (m) cc_final: 0.8356 (m) REVERT: C 571 ASP cc_start: 0.7782 (t0) cc_final: 0.7440 (t0) REVERT: C 633 TRP cc_start: 0.8451 (p-90) cc_final: 0.8208 (p-90) REVERT: C 737 ASP cc_start: 0.7904 (t0) cc_final: 0.7658 (t0) REVERT: C 751 ASN cc_start: 0.8887 (m110) cc_final: 0.8655 (m-40) REVERT: C 979 ASP cc_start: 0.7839 (t0) cc_final: 0.7558 (t0) REVERT: C 1002 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7569 (mm-40) REVERT: C 1017 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7610 (tm-30) outliers start: 28 outliers final: 9 residues processed: 671 average time/residue: 0.1962 time to fit residues: 204.1333 Evaluate side-chains 544 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 534 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 580 GLN A 607 GLN A 613 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN B 30 ASN B 196 ASN B 218 GLN B 317 ASN B 764 ASN B 856 ASN B1002 GLN C 30 ASN C 81 ASN C 99 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN C 245 HIS C 751 ASN C 856 ASN C 907 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.104344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.083617 restraints weight = 60562.239| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.27 r_work: 0.3106 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28490 Z= 0.187 Angle : 0.833 15.169 38970 Z= 0.404 Chirality : 0.049 0.594 4679 Planarity : 0.005 0.060 4827 Dihedral : 13.649 110.746 5964 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.25 % Favored : 95.63 % Rotamer: Outliers : 1.37 % Allowed : 8.99 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3321 helix: 0.85 (0.19), residues: 750 sheet: 0.07 (0.19), residues: 705 loop : -1.29 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 567 TYR 0.021 0.002 TYR C1067 PHE 0.025 0.002 PHE A 823 TRP 0.016 0.002 TRP A 64 HIS 0.006 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00420 (28332) covalent geometry : angle 0.78094 (38541) SS BOND : bond 0.00394 ( 45) SS BOND : angle 1.50853 ( 90) hydrogen bonds : bond 0.04728 ( 1114) hydrogen bonds : angle 6.40425 ( 3111) link_ALPHA1-4 : bond 0.01298 ( 21) link_ALPHA1-4 : angle 2.67830 ( 63) link_BETA1-4 : bond 0.00426 ( 33) link_BETA1-4 : angle 2.01017 ( 99) link_BETA1-6 : bond 0.01778 ( 3) link_BETA1-6 : angle 1.89020 ( 9) link_NAG-ASN : bond 0.00478 ( 56) link_NAG-ASN : angle 3.80427 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 542 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9152 (mp) cc_final: 0.8802 (mt) REVERT: A 100 ILE cc_start: 0.8981 (mt) cc_final: 0.8591 (mp) REVERT: A 121 ASN cc_start: 0.6749 (OUTLIER) cc_final: 0.6332 (t0) REVERT: A 138 ASP cc_start: 0.9106 (t0) cc_final: 0.8871 (t0) REVERT: A 190 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7463 (mtt180) REVERT: A 191 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 207 HIS cc_start: 0.7501 (m170) cc_final: 0.7135 (m170) REVERT: A 319 ARG cc_start: 0.8574 (ptp-170) cc_final: 0.8348 (ptp90) REVERT: A 406 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7614 (mt-10) REVERT: A 414 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8103 (mm-40) REVERT: A 453 TYR cc_start: 0.7627 (p90) cc_final: 0.6819 (p90) REVERT: A 539 VAL cc_start: 0.9183 (m) cc_final: 0.8849 (t) REVERT: A 564 GLN cc_start: 0.8581 (tp40) cc_final: 0.8330 (tp40) REVERT: A 571 ASP cc_start: 0.8039 (t0) cc_final: 0.7661 (t70) REVERT: A 574 ASP cc_start: 0.8585 (t70) cc_final: 0.8152 (t0) REVERT: A 735 SER cc_start: 0.9029 (t) cc_final: 0.8382 (p) REVERT: A 773 GLU cc_start: 0.8557 (tp30) cc_final: 0.8043 (mt-10) REVERT: A 780 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8240 (mt-10) REVERT: A 796 ASP cc_start: 0.8438 (t0) cc_final: 0.8236 (t0) REVERT: A 820 ASP cc_start: 0.8735 (m-30) cc_final: 0.8499 (m-30) REVERT: A 979 ASP cc_start: 0.8467 (t0) cc_final: 0.8134 (t0) REVERT: A 994 ASP cc_start: 0.8588 (t70) cc_final: 0.8341 (t0) REVERT: A 1019 ARG cc_start: 0.8332 (ttp-110) cc_final: 0.8108 (ttp-110) REVERT: A 1072 GLU cc_start: 0.8838 (pm20) cc_final: 0.8600 (pm20) REVERT: A 1092 GLU cc_start: 0.7874 (pm20) cc_final: 0.7543 (pm20) REVERT: B 99 ASN cc_start: 0.8560 (t0) cc_final: 0.8175 (t0) REVERT: B 132 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7645 (mt-10) REVERT: B 153 MET cc_start: 0.8497 (ppp) cc_final: 0.8199 (ppp) REVERT: B 190 ARG cc_start: 0.8436 (tpp-160) cc_final: 0.7606 (mmt180) REVERT: B 314 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: B 453 TYR cc_start: 0.7923 (p90) cc_final: 0.6961 (p90) REVERT: B 586 ASP cc_start: 0.8236 (t0) cc_final: 0.7921 (t0) REVERT: B 661 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 735 SER cc_start: 0.8797 (t) cc_final: 0.8256 (p) REVERT: B 787 GLN cc_start: 0.8630 (mp10) cc_final: 0.8342 (mm-40) REVERT: B 790 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8106 (mtpp) REVERT: B 796 ASP cc_start: 0.8285 (t0) cc_final: 0.7914 (t0) REVERT: B 804 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8438 (mt0) REVERT: B 825 LYS cc_start: 0.8890 (mmpt) cc_final: 0.8543 (mmmt) REVERT: B 867 ASP cc_start: 0.8430 (m-30) cc_final: 0.8174 (m-30) REVERT: B 902 MET cc_start: 0.9004 (mmm) cc_final: 0.8798 (tpt) REVERT: B 918 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8055 (mt-10) REVERT: B 979 ASP cc_start: 0.8567 (t0) cc_final: 0.8286 (t0) REVERT: B 1072 GLU cc_start: 0.8736 (pm20) cc_final: 0.8506 (pm20) REVERT: B 1092 GLU cc_start: 0.7731 (pm20) cc_final: 0.7524 (pm20) REVERT: C 52 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8483 (tm-30) REVERT: C 54 LEU cc_start: 0.9158 (mt) cc_final: 0.8949 (mt) REVERT: C 100 ILE cc_start: 0.9116 (mp) cc_final: 0.8889 (mp) REVERT: C 129 LYS cc_start: 0.8252 (tttt) cc_final: 0.7966 (ttmm) REVERT: C 132 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 188 ASN cc_start: 0.8455 (t0) cc_final: 0.8129 (t0) REVERT: C 191 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7517 (mt-10) REVERT: C 200 TYR cc_start: 0.7854 (m-80) cc_final: 0.7537 (m-80) REVERT: C 354 ASN cc_start: 0.8629 (t0) cc_final: 0.8370 (t0) REVERT: C 571 ASP cc_start: 0.8239 (t0) cc_final: 0.7976 (t70) REVERT: C 737 ASP cc_start: 0.8146 (t0) cc_final: 0.7642 (t0) REVERT: C 790 LYS cc_start: 0.8367 (mmtm) cc_final: 0.8136 (mmtm) REVERT: C 1148 PHE cc_start: 0.7353 (t80) cc_final: 0.6931 (t80) outliers start: 40 outliers final: 20 residues processed: 567 average time/residue: 0.1804 time to fit residues: 159.4664 Evaluate side-chains 516 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 494 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 171 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 311 optimal weight: 0.3980 chunk 147 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 308 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 317 ASN A 607 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 196 ASN B 417 ASN B 655 HIS C 146 HIS ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 779 GLN C1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081877 restraints weight = 60975.586| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.30 r_work: 0.3070 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28490 Z= 0.215 Angle : 0.782 14.640 38970 Z= 0.377 Chirality : 0.048 0.546 4679 Planarity : 0.004 0.065 4827 Dihedral : 12.578 107.386 5948 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.09 % Favored : 94.79 % Rotamer: Outliers : 2.20 % Allowed : 10.30 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3321 helix: 1.34 (0.20), residues: 750 sheet: 0.08 (0.19), residues: 720 loop : -1.34 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 509 TYR 0.029 0.002 TYR B 473 PHE 0.020 0.002 PHE A 175 TRP 0.010 0.001 TRP A 633 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00490 (28332) covalent geometry : angle 0.73791 (38541) SS BOND : bond 0.00562 ( 45) SS BOND : angle 1.57932 ( 90) hydrogen bonds : bond 0.04452 ( 1114) hydrogen bonds : angle 6.07061 ( 3111) link_ALPHA1-4 : bond 0.01551 ( 21) link_ALPHA1-4 : angle 2.71210 ( 63) link_BETA1-4 : bond 0.00283 ( 33) link_BETA1-4 : angle 1.66825 ( 99) link_BETA1-6 : bond 0.01448 ( 3) link_BETA1-6 : angle 1.85676 ( 9) link_NAG-ASN : bond 0.00376 ( 56) link_NAG-ASN : angle 3.31451 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 498 time to evaluate : 0.702 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 54 LEU cc_start: 0.9108 (mp) cc_final: 0.8893 (mt) REVERT: A 100 ILE cc_start: 0.8957 (mt) cc_final: 0.8639 (mp) REVERT: A 190 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7393 (mtt180) REVERT: A 191 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7979 (mt-10) REVERT: A 207 HIS cc_start: 0.7543 (m170) cc_final: 0.7159 (m170) REVERT: A 319 ARG cc_start: 0.8630 (ptp-170) cc_final: 0.8388 (ptp90) REVERT: A 453 TYR cc_start: 0.7674 (p90) cc_final: 0.6994 (p90) REVERT: A 539 VAL cc_start: 0.9202 (m) cc_final: 0.8896 (t) REVERT: A 571 ASP cc_start: 0.8094 (t0) cc_final: 0.7709 (t70) REVERT: A 574 ASP cc_start: 0.8603 (t70) cc_final: 0.8144 (t0) REVERT: A 646 ARG cc_start: 0.8899 (mtm-85) cc_final: 0.8647 (mtm-85) REVERT: A 702 GLU cc_start: 0.8355 (tt0) cc_final: 0.8073 (tp30) REVERT: A 735 SER cc_start: 0.9054 (t) cc_final: 0.8378 (p) REVERT: A 773 GLU cc_start: 0.8614 (tp30) cc_final: 0.8133 (tt0) REVERT: A 780 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8195 (mt-10) REVERT: A 796 ASP cc_start: 0.8486 (t0) cc_final: 0.8254 (t0) REVERT: A 820 ASP cc_start: 0.8686 (m-30) cc_final: 0.8421 (m-30) REVERT: A 979 ASP cc_start: 0.8521 (t0) cc_final: 0.8239 (t0) REVERT: A 994 ASP cc_start: 0.8570 (t70) cc_final: 0.8273 (t0) REVERT: A 1019 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.8114 (ttp-110) REVERT: A 1045 LYS cc_start: 0.8552 (tppt) cc_final: 0.8323 (tppt) REVERT: A 1072 GLU cc_start: 0.8863 (pm20) cc_final: 0.8652 (pm20) REVERT: B 140 PHE cc_start: 0.8703 (p90) cc_final: 0.8419 (p90) REVERT: B 190 ARG cc_start: 0.8501 (tpp-160) cc_final: 0.7593 (mmt180) REVERT: B 207 HIS cc_start: 0.7468 (m170) cc_final: 0.7021 (m170) REVERT: B 314 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8164 (tm-30) REVERT: B 414 GLN cc_start: 0.8236 (mp10) cc_final: 0.7859 (mp10) REVERT: B 586 ASP cc_start: 0.8287 (t0) cc_final: 0.8028 (t0) REVERT: B 661 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7531 (tm-30) REVERT: B 735 SER cc_start: 0.8878 (t) cc_final: 0.8627 (t) REVERT: B 748 GLU cc_start: 0.8079 (pm20) cc_final: 0.7810 (pm20) REVERT: B 786 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7910 (mmmt) REVERT: B 790 LYS cc_start: 0.8492 (mtpt) cc_final: 0.8182 (mtpp) REVERT: B 804 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8289 (mt0) REVERT: B 825 LYS cc_start: 0.8890 (mmpt) cc_final: 0.8660 (mmtt) REVERT: B 867 ASP cc_start: 0.8473 (m-30) cc_final: 0.8254 (m-30) REVERT: B 979 ASP cc_start: 0.8599 (t0) cc_final: 0.8342 (t0) REVERT: B 1072 GLU cc_start: 0.8827 (pm20) cc_final: 0.8613 (pm20) REVERT: B 1092 GLU cc_start: 0.7837 (pm20) cc_final: 0.7622 (pm20) REVERT: C 52 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8551 (tm-30) REVERT: C 100 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8815 (mp) REVERT: C 129 LYS cc_start: 0.8256 (tttt) cc_final: 0.7970 (ttmm) REVERT: C 132 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7747 (mt-10) REVERT: C 191 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7572 (mt-10) REVERT: C 237 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8637 (mtm-85) REVERT: C 354 ASN cc_start: 0.8609 (t0) cc_final: 0.8339 (t0) REVERT: C 455 LEU cc_start: 0.9179 (tp) cc_final: 0.8904 (tp) REVERT: C 516 GLU cc_start: 0.7790 (pm20) cc_final: 0.7515 (pm20) REVERT: C 571 ASP cc_start: 0.8281 (t0) cc_final: 0.7934 (t70) outliers start: 64 outliers final: 37 residues processed: 529 average time/residue: 0.1746 time to fit residues: 146.6984 Evaluate side-chains 506 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 467 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 146 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 280 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1119 ASN B 30 ASN B 121 ASN B 196 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 779 GLN C 872 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.102951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082051 restraints weight = 60553.169| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.30 r_work: 0.3082 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28490 Z= 0.193 Angle : 0.756 14.279 38970 Z= 0.359 Chirality : 0.046 0.544 4679 Planarity : 0.004 0.067 4827 Dihedral : 11.712 105.076 5946 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 2.40 % Allowed : 11.57 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3321 helix: 1.49 (0.20), residues: 750 sheet: 0.13 (0.20), residues: 687 loop : -1.33 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 509 TYR 0.022 0.001 TYR C1067 PHE 0.040 0.002 PHE B1148 TRP 0.008 0.001 TRP C 152 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00436 (28332) covalent geometry : angle 0.71631 (38541) SS BOND : bond 0.00374 ( 45) SS BOND : angle 1.32484 ( 90) hydrogen bonds : bond 0.04151 ( 1114) hydrogen bonds : angle 5.94928 ( 3111) link_ALPHA1-4 : bond 0.01611 ( 21) link_ALPHA1-4 : angle 2.76951 ( 63) link_BETA1-4 : bond 0.00257 ( 33) link_BETA1-4 : angle 1.49575 ( 99) link_BETA1-6 : bond 0.01442 ( 3) link_BETA1-6 : angle 1.99248 ( 9) link_NAG-ASN : bond 0.00354 ( 56) link_NAG-ASN : angle 3.09345 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 485 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8953 (mt) cc_final: 0.8611 (mp) REVERT: A 121 ASN cc_start: 0.6534 (t0) cc_final: 0.6315 (t0) REVERT: A 140 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7922 (p90) REVERT: A 190 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7334 (mtt180) REVERT: A 207 HIS cc_start: 0.7519 (m170) cc_final: 0.7122 (m170) REVERT: A 319 ARG cc_start: 0.8628 (ptp-170) cc_final: 0.8380 (ptp90) REVERT: A 406 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 422 ASN cc_start: 0.8556 (p0) cc_final: 0.8236 (p0) REVERT: A 571 ASP cc_start: 0.8136 (t0) cc_final: 0.7783 (t70) REVERT: A 574 ASP cc_start: 0.8562 (t70) cc_final: 0.8085 (t0) REVERT: A 646 ARG cc_start: 0.8879 (mtm-85) cc_final: 0.8663 (mtm-85) REVERT: A 702 GLU cc_start: 0.8312 (tt0) cc_final: 0.7917 (tp30) REVERT: A 735 SER cc_start: 0.9080 (t) cc_final: 0.8837 (t) REVERT: A 740 MET cc_start: 0.9010 (ttm) cc_final: 0.8700 (ttp) REVERT: A 773 GLU cc_start: 0.8584 (tp30) cc_final: 0.8096 (tt0) REVERT: A 780 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8103 (mt-10) REVERT: A 796 ASP cc_start: 0.8505 (t0) cc_final: 0.8266 (t0) REVERT: A 820 ASP cc_start: 0.8669 (m-30) cc_final: 0.8397 (m-30) REVERT: A 935 GLN cc_start: 0.8524 (tt0) cc_final: 0.8272 (tt0) REVERT: A 979 ASP cc_start: 0.8534 (t0) cc_final: 0.8257 (t0) REVERT: A 994 ASP cc_start: 0.8526 (t70) cc_final: 0.8234 (t0) REVERT: A 1045 LYS cc_start: 0.8575 (tppt) cc_final: 0.8365 (tppt) REVERT: B 140 PHE cc_start: 0.8760 (p90) cc_final: 0.8433 (p90) REVERT: B 190 ARG cc_start: 0.8469 (tpp-160) cc_final: 0.7660 (mmt180) REVERT: B 314 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8182 (tm-30) REVERT: B 414 GLN cc_start: 0.8261 (mp10) cc_final: 0.7860 (mp10) REVERT: B 661 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7528 (tm-30) REVERT: B 735 SER cc_start: 0.8869 (t) cc_final: 0.8628 (t) REVERT: B 786 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7949 (mmmt) REVERT: B 790 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8271 (mtpp) REVERT: B 804 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8328 (mt0) REVERT: B 825 LYS cc_start: 0.8888 (mmpt) cc_final: 0.8684 (mmtt) REVERT: B 867 ASP cc_start: 0.8471 (m-30) cc_final: 0.8216 (m-30) REVERT: B 869 MET cc_start: 0.9038 (mtm) cc_final: 0.8791 (mtp) REVERT: B 918 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 979 ASP cc_start: 0.8593 (t0) cc_final: 0.8328 (t0) REVERT: B 1072 GLU cc_start: 0.8813 (pm20) cc_final: 0.8594 (pm20) REVERT: B 1092 GLU cc_start: 0.7861 (pm20) cc_final: 0.7638 (pm20) REVERT: C 100 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8776 (mp) REVERT: C 354 ASN cc_start: 0.8583 (t0) cc_final: 0.8322 (t0) REVERT: C 571 ASP cc_start: 0.8267 (t0) cc_final: 0.7897 (t70) REVERT: C 702 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7975 (tm-30) REVERT: C 737 ASP cc_start: 0.8343 (t0) cc_final: 0.8017 (t0) REVERT: C 790 LYS cc_start: 0.8510 (mmtm) cc_final: 0.8032 (mmtm) outliers start: 70 outliers final: 43 residues processed: 526 average time/residue: 0.1683 time to fit residues: 140.1890 Evaluate side-chains 506 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 461 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 293 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 287 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 260 optimal weight: 0.9980 chunk 249 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A1002 GLN B 30 ASN B 146 HIS B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 644 GLN C 779 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.102598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082177 restraints weight = 60412.494| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.27 r_work: 0.3076 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28490 Z= 0.175 Angle : 0.756 14.993 38970 Z= 0.354 Chirality : 0.046 0.538 4679 Planarity : 0.004 0.067 4827 Dihedral : 10.740 102.758 5942 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 2.85 % Allowed : 12.22 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3321 helix: 1.61 (0.20), residues: 750 sheet: 0.08 (0.19), residues: 702 loop : -1.32 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 454 TYR 0.021 0.001 TYR C1067 PHE 0.034 0.002 PHE A1148 TRP 0.005 0.001 TRP C 152 HIS 0.008 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00390 (28332) covalent geometry : angle 0.71289 (38541) SS BOND : bond 0.00416 ( 45) SS BOND : angle 1.26758 ( 90) hydrogen bonds : bond 0.03981 ( 1114) hydrogen bonds : angle 5.84829 ( 3111) link_ALPHA1-4 : bond 0.01747 ( 21) link_ALPHA1-4 : angle 2.75189 ( 63) link_BETA1-4 : bond 0.00386 ( 33) link_BETA1-4 : angle 1.46611 ( 99) link_BETA1-6 : bond 0.01436 ( 3) link_BETA1-6 : angle 2.07030 ( 9) link_NAG-ASN : bond 0.00399 ( 56) link_NAG-ASN : angle 3.26924 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 480 time to evaluate : 0.707 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 54 LEU cc_start: 0.9129 (mp) cc_final: 0.8803 (mt) REVERT: A 100 ILE cc_start: 0.8924 (mt) cc_final: 0.8573 (mp) REVERT: A 190 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7260 (mtt180) REVERT: A 191 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7766 (mm-30) REVERT: A 207 HIS cc_start: 0.7545 (m170) cc_final: 0.7020 (m-70) REVERT: A 246 ARG cc_start: 0.7494 (ttp-110) cc_final: 0.7241 (ttp-110) REVERT: A 319 ARG cc_start: 0.8647 (ptp-170) cc_final: 0.8401 (ptp90) REVERT: A 394 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.8046 (p0) REVERT: A 406 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7628 (mt-10) REVERT: A 571 ASP cc_start: 0.8191 (t0) cc_final: 0.7829 (t70) REVERT: A 574 ASP cc_start: 0.8534 (t70) cc_final: 0.8040 (t0) REVERT: A 646 ARG cc_start: 0.8877 (mtm-85) cc_final: 0.8662 (mtm-85) REVERT: A 740 MET cc_start: 0.8972 (ttm) cc_final: 0.8653 (ttp) REVERT: A 773 GLU cc_start: 0.8592 (tp30) cc_final: 0.8048 (tt0) REVERT: A 780 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8334 (mt-10) REVERT: A 796 ASP cc_start: 0.8508 (t0) cc_final: 0.8254 (t0) REVERT: A 820 ASP cc_start: 0.8654 (m-30) cc_final: 0.8370 (m-30) REVERT: A 851 CYS cc_start: 0.7327 (t) cc_final: 0.7023 (t) REVERT: A 855 PHE cc_start: 0.8889 (m-80) cc_final: 0.8256 (m-80) REVERT: A 935 GLN cc_start: 0.8530 (tt0) cc_final: 0.8242 (tt0) REVERT: A 979 ASP cc_start: 0.8593 (t0) cc_final: 0.8306 (t0) REVERT: A 994 ASP cc_start: 0.8525 (t70) cc_final: 0.8214 (t0) REVERT: A 1045 LYS cc_start: 0.8599 (tppt) cc_final: 0.8388 (tppt) REVERT: A 1072 GLU cc_start: 0.8739 (pm20) cc_final: 0.8513 (pm20) REVERT: A 1107 ARG cc_start: 0.8252 (mpt-90) cc_final: 0.7978 (mpt180) REVERT: B 140 PHE cc_start: 0.8768 (p90) cc_final: 0.8428 (p90) REVERT: B 145 TYR cc_start: 0.5070 (OUTLIER) cc_final: 0.2606 (p90) REVERT: B 153 MET cc_start: 0.8254 (ppp) cc_final: 0.7919 (ppp) REVERT: B 190 ARG cc_start: 0.8511 (tpp-160) cc_final: 0.7613 (mmt180) REVERT: B 314 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8229 (tm-30) REVERT: B 414 GLN cc_start: 0.8240 (mp10) cc_final: 0.7812 (mp10) REVERT: B 661 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7437 (tm-30) REVERT: B 735 SER cc_start: 0.8841 (t) cc_final: 0.8589 (t) REVERT: B 786 LYS cc_start: 0.8278 (mmmt) cc_final: 0.8028 (mmmt) REVERT: B 790 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8196 (mtpp) REVERT: B 804 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8307 (mt0) REVERT: B 867 ASP cc_start: 0.8498 (m-30) cc_final: 0.8223 (m-30) REVERT: B 869 MET cc_start: 0.9026 (mtm) cc_final: 0.8788 (mtp) REVERT: B 979 ASP cc_start: 0.8613 (t0) cc_final: 0.8352 (t0) REVERT: B 1072 GLU cc_start: 0.8823 (pm20) cc_final: 0.8591 (pm20) REVERT: C 100 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8731 (mp) REVERT: C 121 ASN cc_start: 0.7166 (t0) cc_final: 0.6578 (t0) REVERT: C 191 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7733 (mt-10) REVERT: C 354 ASN cc_start: 0.8563 (t0) cc_final: 0.8279 (t0) REVERT: C 571 ASP cc_start: 0.8309 (t0) cc_final: 0.7932 (t70) REVERT: C 702 GLU cc_start: 0.8246 (tm-30) cc_final: 0.8022 (tm-30) REVERT: C 737 ASP cc_start: 0.8400 (t0) cc_final: 0.8107 (t0) REVERT: C 790 LYS cc_start: 0.8547 (mmtm) cc_final: 0.8214 (mmtm) REVERT: C 1125 ASN cc_start: 0.8838 (p0) cc_final: 0.8527 (p0) outliers start: 83 outliers final: 49 residues processed: 528 average time/residue: 0.1701 time to fit residues: 142.6139 Evaluate side-chains 517 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 465 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 242 optimal weight: 0.0170 chunk 183 optimal weight: 0.8980 chunk 211 optimal weight: 0.0670 chunk 204 optimal weight: 3.9990 chunk 250 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 30 ASN B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082758 restraints weight = 60345.086| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.30 r_work: 0.3092 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28490 Z= 0.146 Angle : 0.733 14.439 38970 Z= 0.343 Chirality : 0.045 0.530 4679 Planarity : 0.004 0.061 4827 Dihedral : 9.787 100.504 5942 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 2.44 % Allowed : 13.59 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3321 helix: 1.73 (0.20), residues: 753 sheet: 0.03 (0.20), residues: 693 loop : -1.23 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 634 TYR 0.021 0.001 TYR A 473 PHE 0.027 0.001 PHE C 456 TRP 0.005 0.001 TRP B 633 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00320 (28332) covalent geometry : angle 0.68982 (38541) SS BOND : bond 0.00349 ( 45) SS BOND : angle 1.27893 ( 90) hydrogen bonds : bond 0.03766 ( 1114) hydrogen bonds : angle 5.73317 ( 3111) link_ALPHA1-4 : bond 0.01831 ( 21) link_ALPHA1-4 : angle 2.90385 ( 63) link_BETA1-4 : bond 0.00313 ( 33) link_BETA1-4 : angle 1.36561 ( 99) link_BETA1-6 : bond 0.01607 ( 3) link_BETA1-6 : angle 2.22837 ( 9) link_NAG-ASN : bond 0.00481 ( 56) link_NAG-ASN : angle 3.15773 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 493 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8538 (p0) REVERT: A 100 ILE cc_start: 0.8939 (mt) cc_final: 0.8643 (mp) REVERT: A 140 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8118 (p90) REVERT: A 190 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7260 (mtt180) REVERT: A 207 HIS cc_start: 0.7525 (m170) cc_final: 0.7000 (m-70) REVERT: A 319 ARG cc_start: 0.8641 (ptp-170) cc_final: 0.8406 (ptp90) REVERT: A 406 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 571 ASP cc_start: 0.8179 (t0) cc_final: 0.7783 (t70) REVERT: A 574 ASP cc_start: 0.8512 (t70) cc_final: 0.8029 (t0) REVERT: A 646 ARG cc_start: 0.8882 (mtm-85) cc_final: 0.8671 (mtm-85) REVERT: A 773 GLU cc_start: 0.8585 (tp30) cc_final: 0.8049 (tt0) REVERT: A 780 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8140 (mt-10) REVERT: A 796 ASP cc_start: 0.8505 (t0) cc_final: 0.8242 (t0) REVERT: A 820 ASP cc_start: 0.8623 (m-30) cc_final: 0.8341 (m-30) REVERT: A 979 ASP cc_start: 0.8609 (t0) cc_final: 0.8322 (t0) REVERT: A 994 ASP cc_start: 0.8510 (t70) cc_final: 0.8191 (t0) REVERT: A 1045 LYS cc_start: 0.8590 (tppt) cc_final: 0.8386 (tppt) REVERT: A 1072 GLU cc_start: 0.8726 (pm20) cc_final: 0.8511 (pm20) REVERT: A 1146 ASP cc_start: 0.7737 (m-30) cc_final: 0.7443 (m-30) REVERT: B 140 PHE cc_start: 0.8758 (p90) cc_final: 0.8399 (p90) REVERT: B 145 TYR cc_start: 0.5040 (OUTLIER) cc_final: 0.2525 (p90) REVERT: B 153 MET cc_start: 0.8130 (ppp) cc_final: 0.7861 (ppp) REVERT: B 190 ARG cc_start: 0.8507 (tpp-160) cc_final: 0.7610 (mmt180) REVERT: B 314 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8257 (tm-30) REVERT: B 414 GLN cc_start: 0.8217 (mp10) cc_final: 0.7774 (mp10) REVERT: B 453 TYR cc_start: 0.7756 (p90) cc_final: 0.7367 (p90) REVERT: B 735 SER cc_start: 0.8794 (t) cc_final: 0.8541 (t) REVERT: B 786 LYS cc_start: 0.8268 (mmmt) cc_final: 0.8022 (mmmt) REVERT: B 790 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8269 (mtpp) REVERT: B 804 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8300 (mt0) REVERT: B 867 ASP cc_start: 0.8486 (m-30) cc_final: 0.8213 (m-30) REVERT: B 979 ASP cc_start: 0.8604 (t0) cc_final: 0.8348 (t0) REVERT: B 1072 GLU cc_start: 0.8806 (pm20) cc_final: 0.8556 (pm20) REVERT: C 100 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8698 (mp) REVERT: C 121 ASN cc_start: 0.7022 (t0) cc_final: 0.6439 (t0) REVERT: C 354 ASN cc_start: 0.8552 (t0) cc_final: 0.8270 (t0) REVERT: C 571 ASP cc_start: 0.8299 (t0) cc_final: 0.7915 (t70) REVERT: C 702 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7958 (tm-30) REVERT: C 737 ASP cc_start: 0.8409 (t0) cc_final: 0.8098 (t0) REVERT: C 1125 ASN cc_start: 0.8826 (p0) cc_final: 0.8546 (p0) outliers start: 71 outliers final: 45 residues processed: 532 average time/residue: 0.1731 time to fit residues: 147.3525 Evaluate side-chains 525 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 476 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 284 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 299 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 30 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.102788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082122 restraints weight = 60303.343| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.29 r_work: 0.3077 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28490 Z= 0.183 Angle : 0.749 13.866 38970 Z= 0.352 Chirality : 0.046 0.514 4679 Planarity : 0.004 0.063 4827 Dihedral : 8.887 95.875 5942 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.52 % Rotamer: Outliers : 2.54 % Allowed : 14.49 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3321 helix: 1.70 (0.20), residues: 753 sheet: 0.02 (0.19), residues: 708 loop : -1.25 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 454 TYR 0.020 0.001 TYR C1067 PHE 0.018 0.002 PHE A 133 TRP 0.009 0.001 TRP C 152 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00412 (28332) covalent geometry : angle 0.70703 (38541) SS BOND : bond 0.00355 ( 45) SS BOND : angle 1.23830 ( 90) hydrogen bonds : bond 0.03885 ( 1114) hydrogen bonds : angle 5.72227 ( 3111) link_ALPHA1-4 : bond 0.01893 ( 21) link_ALPHA1-4 : angle 2.92167 ( 63) link_BETA1-4 : bond 0.00318 ( 33) link_BETA1-4 : angle 1.47970 ( 99) link_BETA1-6 : bond 0.01527 ( 3) link_BETA1-6 : angle 2.32244 ( 9) link_NAG-ASN : bond 0.00367 ( 56) link_NAG-ASN : angle 3.11437 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 487 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8586 (p0) REVERT: A 100 ILE cc_start: 0.8974 (mt) cc_final: 0.8677 (mp) REVERT: A 140 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8101 (p90) REVERT: A 141 LEU cc_start: 0.8426 (mp) cc_final: 0.8181 (mp) REVERT: A 190 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7283 (mtt180) REVERT: A 207 HIS cc_start: 0.7532 (m170) cc_final: 0.6930 (m-70) REVERT: A 281 GLU cc_start: 0.8420 (pp20) cc_final: 0.8150 (pp20) REVERT: A 319 ARG cc_start: 0.8619 (ptp-170) cc_final: 0.8401 (ptp90) REVERT: A 406 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 571 ASP cc_start: 0.8212 (t0) cc_final: 0.7788 (t70) REVERT: A 574 ASP cc_start: 0.8511 (t70) cc_final: 0.8017 (t0) REVERT: A 646 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8698 (mtm-85) REVERT: A 702 GLU cc_start: 0.8322 (tt0) cc_final: 0.7896 (tp30) REVERT: A 740 MET cc_start: 0.9040 (ttm) cc_final: 0.8762 (ttm) REVERT: A 773 GLU cc_start: 0.8571 (tp30) cc_final: 0.8053 (tt0) REVERT: A 780 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8353 (mt-10) REVERT: A 796 ASP cc_start: 0.8515 (t0) cc_final: 0.8244 (t0) REVERT: A 820 ASP cc_start: 0.8639 (m-30) cc_final: 0.8337 (m-30) REVERT: A 855 PHE cc_start: 0.8910 (m-10) cc_final: 0.8632 (m-10) REVERT: A 867 ASP cc_start: 0.8391 (m-30) cc_final: 0.8115 (m-30) REVERT: A 979 ASP cc_start: 0.8633 (t0) cc_final: 0.8339 (t0) REVERT: A 994 ASP cc_start: 0.8529 (t70) cc_final: 0.8245 (t0) REVERT: A 1045 LYS cc_start: 0.8594 (tppt) cc_final: 0.8392 (tppt) REVERT: A 1146 ASP cc_start: 0.7754 (m-30) cc_final: 0.7481 (m-30) REVERT: B 140 PHE cc_start: 0.8777 (p90) cc_final: 0.8408 (p90) REVERT: B 145 TYR cc_start: 0.5001 (OUTLIER) cc_final: 0.2408 (p90) REVERT: B 153 MET cc_start: 0.8101 (ppp) cc_final: 0.7886 (ppp) REVERT: B 190 ARG cc_start: 0.8516 (tpp-160) cc_final: 0.7616 (mmt180) REVERT: B 314 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8317 (tm-30) REVERT: B 414 GLN cc_start: 0.8242 (mp10) cc_final: 0.7799 (mp10) REVERT: B 441 LEU cc_start: 0.8978 (mm) cc_final: 0.8753 (tt) REVERT: B 453 TYR cc_start: 0.7636 (p90) cc_final: 0.7257 (p90) REVERT: B 516 GLU cc_start: 0.7639 (pm20) cc_final: 0.7244 (pm20) REVERT: B 735 SER cc_start: 0.8849 (t) cc_final: 0.8586 (t) REVERT: B 773 GLU cc_start: 0.8286 (tt0) cc_final: 0.7990 (tt0) REVERT: B 786 LYS cc_start: 0.8334 (mmmt) cc_final: 0.8126 (mmmt) REVERT: B 790 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8191 (mtpp) REVERT: B 804 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8150 (mt0) REVERT: B 823 PHE cc_start: 0.8070 (m-80) cc_final: 0.7521 (m-80) REVERT: B 867 ASP cc_start: 0.8519 (m-30) cc_final: 0.8170 (m-30) REVERT: B 979 ASP cc_start: 0.8633 (t0) cc_final: 0.8383 (t0) REVERT: B 1072 GLU cc_start: 0.8833 (pm20) cc_final: 0.8580 (pm20) REVERT: C 100 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8715 (mp) REVERT: C 121 ASN cc_start: 0.7025 (t0) cc_final: 0.6544 (t0) REVERT: C 191 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7777 (mt-10) REVERT: C 273 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7952 (mmt90) REVERT: C 354 ASN cc_start: 0.8518 (t0) cc_final: 0.8250 (t0) REVERT: C 571 ASP cc_start: 0.8327 (t0) cc_final: 0.7998 (t70) REVERT: C 737 ASP cc_start: 0.8452 (t0) cc_final: 0.8140 (t0) REVERT: C 790 LYS cc_start: 0.8594 (mmtm) cc_final: 0.8073 (mmtm) REVERT: C 804 GLN cc_start: 0.8883 (mm110) cc_final: 0.8383 (mm-40) REVERT: C 883 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.8996 (p) REVERT: C 935 GLN cc_start: 0.8410 (tt0) cc_final: 0.8036 (tt0) REVERT: C 1125 ASN cc_start: 0.8831 (p0) cc_final: 0.8607 (p0) REVERT: C 1149 LYS cc_start: 0.8722 (tmtt) cc_final: 0.8003 (mttt) outliers start: 74 outliers final: 56 residues processed: 532 average time/residue: 0.1777 time to fit residues: 151.0741 Evaluate side-chains 528 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 467 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 292 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 chunk 125 optimal weight: 0.0070 chunk 139 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 270 optimal weight: 0.6980 chunk 225 optimal weight: 0.7980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 955 ASN A1119 ASN B 30 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083015 restraints weight = 60394.105| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.30 r_work: 0.3094 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28490 Z= 0.151 Angle : 0.732 14.143 38970 Z= 0.344 Chirality : 0.045 0.516 4679 Planarity : 0.004 0.059 4827 Dihedral : 8.005 93.529 5942 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.82 % Favored : 95.06 % Rotamer: Outliers : 2.33 % Allowed : 15.52 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3321 helix: 1.78 (0.20), residues: 753 sheet: 0.07 (0.20), residues: 687 loop : -1.20 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 408 TYR 0.023 0.001 TYR A 473 PHE 0.024 0.001 PHE A 565 TRP 0.010 0.001 TRP C 152 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00335 (28332) covalent geometry : angle 0.69059 (38541) SS BOND : bond 0.00372 ( 45) SS BOND : angle 1.19667 ( 90) hydrogen bonds : bond 0.03683 ( 1114) hydrogen bonds : angle 5.66774 ( 3111) link_ALPHA1-4 : bond 0.01837 ( 21) link_ALPHA1-4 : angle 3.13246 ( 63) link_BETA1-4 : bond 0.00366 ( 33) link_BETA1-4 : angle 1.44000 ( 99) link_BETA1-6 : bond 0.01637 ( 3) link_BETA1-6 : angle 2.44438 ( 9) link_NAG-ASN : bond 0.00488 ( 56) link_NAG-ASN : angle 2.97063 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 488 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8972 (mt) cc_final: 0.8612 (mp) REVERT: A 115 GLN cc_start: 0.8761 (mt0) cc_final: 0.8296 (mp10) REVERT: A 140 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8036 (p90) REVERT: A 190 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7267 (mtt180) REVERT: A 191 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7764 (mm-30) REVERT: A 207 HIS cc_start: 0.7540 (m170) cc_final: 0.7059 (m-70) REVERT: A 281 GLU cc_start: 0.8419 (pp20) cc_final: 0.8151 (pp20) REVERT: A 319 ARG cc_start: 0.8611 (ptp-170) cc_final: 0.8407 (ptp90) REVERT: A 406 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 571 ASP cc_start: 0.8219 (t0) cc_final: 0.7787 (t70) REVERT: A 574 ASP cc_start: 0.8532 (t70) cc_final: 0.8031 (t0) REVERT: A 646 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8693 (mtm-85) REVERT: A 702 GLU cc_start: 0.8325 (tt0) cc_final: 0.7903 (tp30) REVERT: A 740 MET cc_start: 0.9042 (ttm) cc_final: 0.8760 (ttm) REVERT: A 773 GLU cc_start: 0.8562 (tp30) cc_final: 0.8051 (tt0) REVERT: A 780 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8361 (mt-10) REVERT: A 796 ASP cc_start: 0.8510 (t0) cc_final: 0.8227 (t0) REVERT: A 820 ASP cc_start: 0.8632 (m-30) cc_final: 0.8338 (m-30) REVERT: A 907 ASN cc_start: 0.8884 (m110) cc_final: 0.8586 (m-40) REVERT: A 979 ASP cc_start: 0.8651 (t0) cc_final: 0.8362 (t0) REVERT: A 1146 ASP cc_start: 0.7727 (m-30) cc_final: 0.7455 (m-30) REVERT: B 36 VAL cc_start: 0.8913 (t) cc_final: 0.8608 (m) REVERT: B 140 PHE cc_start: 0.8709 (p90) cc_final: 0.8362 (p90) REVERT: B 145 TYR cc_start: 0.5016 (OUTLIER) cc_final: 0.2372 (p90) REVERT: B 190 ARG cc_start: 0.8524 (tpp-160) cc_final: 0.7652 (mmt180) REVERT: B 314 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8310 (tm-30) REVERT: B 414 GLN cc_start: 0.8258 (mp10) cc_final: 0.7824 (mp10) REVERT: B 441 LEU cc_start: 0.8976 (mm) cc_final: 0.8741 (tt) REVERT: B 633 TRP cc_start: 0.8549 (p-90) cc_final: 0.8160 (p-90) REVERT: B 735 SER cc_start: 0.8812 (t) cc_final: 0.8553 (t) REVERT: B 786 LYS cc_start: 0.8341 (mmmt) cc_final: 0.8140 (mmmt) REVERT: B 804 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8181 (mm-40) REVERT: B 823 PHE cc_start: 0.8052 (m-80) cc_final: 0.7523 (m-80) REVERT: B 867 ASP cc_start: 0.8529 (m-30) cc_final: 0.8117 (m-30) REVERT: B 979 ASP cc_start: 0.8633 (t0) cc_final: 0.8382 (t0) REVERT: B 1072 GLU cc_start: 0.8805 (pm20) cc_final: 0.8561 (pm20) REVERT: C 100 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8692 (mp) REVERT: C 121 ASN cc_start: 0.6949 (t0) cc_final: 0.6463 (t0) REVERT: C 177 MET cc_start: 0.3632 (mpp) cc_final: 0.2968 (mpp) REVERT: C 191 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7809 (mt-10) REVERT: C 354 ASN cc_start: 0.8521 (t0) cc_final: 0.8258 (t0) REVERT: C 571 ASP cc_start: 0.8322 (t0) cc_final: 0.7986 (t70) REVERT: C 633 TRP cc_start: 0.8717 (p-90) cc_final: 0.8359 (p-90) REVERT: C 702 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7863 (tm-30) REVERT: C 737 ASP cc_start: 0.8460 (t0) cc_final: 0.8126 (t0) REVERT: C 790 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8078 (mmtm) REVERT: C 883 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.8993 (p) REVERT: C 935 GLN cc_start: 0.8397 (tt0) cc_final: 0.8171 (tt0) REVERT: C 1125 ASN cc_start: 0.8834 (p0) cc_final: 0.7567 (p0) REVERT: C 1127 ASP cc_start: 0.8578 (m-30) cc_final: 0.8283 (p0) REVERT: C 1149 LYS cc_start: 0.8637 (tmtt) cc_final: 0.7939 (mttt) outliers start: 68 outliers final: 49 residues processed: 526 average time/residue: 0.1884 time to fit residues: 158.1101 Evaluate side-chains 527 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 474 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 104 optimal weight: 0.5980 chunk 210 optimal weight: 0.0980 chunk 86 optimal weight: 0.0870 chunk 147 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 280 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1119 ASN B 30 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.083538 restraints weight = 60328.703| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.31 r_work: 0.3105 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28490 Z= 0.140 Angle : 0.735 14.213 38970 Z= 0.347 Chirality : 0.046 0.511 4679 Planarity : 0.004 0.059 4827 Dihedral : 7.522 91.237 5942 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 1.99 % Allowed : 16.51 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3321 helix: 1.79 (0.20), residues: 753 sheet: 0.09 (0.20), residues: 687 loop : -1.18 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 408 TYR 0.037 0.001 TYR B 660 PHE 0.024 0.001 PHE A 855 TRP 0.008 0.001 TRP C 152 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00309 (28332) covalent geometry : angle 0.69291 (38541) SS BOND : bond 0.00317 ( 45) SS BOND : angle 1.10512 ( 90) hydrogen bonds : bond 0.03589 ( 1114) hydrogen bonds : angle 5.61745 ( 3111) link_ALPHA1-4 : bond 0.01789 ( 21) link_ALPHA1-4 : angle 3.02373 ( 63) link_BETA1-4 : bond 0.00306 ( 33) link_BETA1-4 : angle 1.42874 ( 99) link_BETA1-6 : bond 0.01765 ( 3) link_BETA1-6 : angle 2.53898 ( 9) link_NAG-ASN : bond 0.00450 ( 56) link_NAG-ASN : angle 3.07077 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 496 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8959 (mt) cc_final: 0.8635 (mp) REVERT: A 140 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7968 (p90) REVERT: A 156 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 190 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7249 (mtt180) REVERT: A 207 HIS cc_start: 0.7533 (m170) cc_final: 0.7057 (m-70) REVERT: A 281 GLU cc_start: 0.8428 (pp20) cc_final: 0.8162 (pp20) REVERT: A 406 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 574 ASP cc_start: 0.8520 (t70) cc_final: 0.8021 (t0) REVERT: A 740 MET cc_start: 0.9011 (ttm) cc_final: 0.8719 (ttm) REVERT: A 773 GLU cc_start: 0.8566 (tp30) cc_final: 0.8035 (tt0) REVERT: A 780 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8348 (mt-10) REVERT: A 796 ASP cc_start: 0.8513 (t0) cc_final: 0.8237 (t0) REVERT: A 820 ASP cc_start: 0.8607 (m-30) cc_final: 0.8308 (m-30) REVERT: A 907 ASN cc_start: 0.8811 (m110) cc_final: 0.8589 (m-40) REVERT: A 979 ASP cc_start: 0.8660 (t0) cc_final: 0.8401 (t0) REVERT: A 1019 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.7833 (ttp-110) REVERT: A 1146 ASP cc_start: 0.7735 (m-30) cc_final: 0.7461 (m-30) REVERT: B 36 VAL cc_start: 0.8905 (t) cc_final: 0.8611 (m) REVERT: B 140 PHE cc_start: 0.8713 (p90) cc_final: 0.8358 (p90) REVERT: B 145 TYR cc_start: 0.4990 (OUTLIER) cc_final: 0.2377 (p90) REVERT: B 190 ARG cc_start: 0.8525 (tpp-160) cc_final: 0.7645 (mmt180) REVERT: B 314 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 414 GLN cc_start: 0.8259 (mp10) cc_final: 0.7829 (mp10) REVERT: B 441 LEU cc_start: 0.8951 (mm) cc_final: 0.8742 (tt) REVERT: B 539 VAL cc_start: 0.9139 (m) cc_final: 0.8685 (t) REVERT: B 633 TRP cc_start: 0.8552 (p-90) cc_final: 0.8152 (p-90) REVERT: B 735 SER cc_start: 0.8789 (t) cc_final: 0.8526 (t) REVERT: B 738 CYS cc_start: 0.7517 (t) cc_final: 0.7159 (t) REVERT: B 786 LYS cc_start: 0.8341 (mmmt) cc_final: 0.8132 (mmmt) REVERT: B 790 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8088 (mtmm) REVERT: B 804 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8215 (mm-40) REVERT: B 823 PHE cc_start: 0.8023 (m-80) cc_final: 0.7512 (m-80) REVERT: B 867 ASP cc_start: 0.8420 (m-30) cc_final: 0.8090 (m-30) REVERT: B 933 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8582 (mtpp) REVERT: B 979 ASP cc_start: 0.8647 (t0) cc_final: 0.8340 (t0) REVERT: B 1072 GLU cc_start: 0.8823 (pm20) cc_final: 0.8578 (pm20) REVERT: C 100 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8685 (mp) REVERT: C 121 ASN cc_start: 0.6939 (t0) cc_final: 0.6442 (t0) REVERT: C 177 MET cc_start: 0.3620 (mpp) cc_final: 0.2983 (mpp) REVERT: C 191 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7808 (mt-10) REVERT: C 354 ASN cc_start: 0.8541 (t0) cc_final: 0.8258 (t0) REVERT: C 571 ASP cc_start: 0.8314 (t0) cc_final: 0.7989 (t70) REVERT: C 633 TRP cc_start: 0.8717 (p-90) cc_final: 0.8339 (p-90) REVERT: C 737 ASP cc_start: 0.8467 (t0) cc_final: 0.8135 (t0) REVERT: C 790 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8432 (mmtm) REVERT: C 796 ASP cc_start: 0.8246 (t0) cc_final: 0.7735 (p0) REVERT: C 804 GLN cc_start: 0.8879 (mm110) cc_final: 0.8548 (mm-40) REVERT: C 883 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.8981 (p) REVERT: C 935 GLN cc_start: 0.8390 (tt0) cc_final: 0.7915 (tt0) REVERT: C 1125 ASN cc_start: 0.8805 (p0) cc_final: 0.7537 (p0) REVERT: C 1127 ASP cc_start: 0.8600 (m-30) cc_final: 0.8327 (p0) REVERT: C 1149 LYS cc_start: 0.8650 (tmtt) cc_final: 0.7972 (mttt) outliers start: 58 outliers final: 45 residues processed: 527 average time/residue: 0.1806 time to fit residues: 151.9364 Evaluate side-chains 528 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 478 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 35 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 239 optimal weight: 3.9990 chunk 309 optimal weight: 0.6980 chunk 216 optimal weight: 0.0040 chunk 319 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 chunk 209 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 30 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.083491 restraints weight = 60320.556| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.31 r_work: 0.3105 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28490 Z= 0.143 Angle : 0.729 13.514 38970 Z= 0.345 Chirality : 0.045 0.503 4679 Planarity : 0.004 0.072 4827 Dihedral : 6.990 88.329 5942 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 1.92 % Allowed : 16.92 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3321 helix: 1.81 (0.20), residues: 756 sheet: 0.09 (0.19), residues: 687 loop : -1.19 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 567 TYR 0.052 0.001 TYR B 660 PHE 0.047 0.001 PHE C1148 TRP 0.007 0.001 TRP C 152 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00318 (28332) covalent geometry : angle 0.68988 (38541) SS BOND : bond 0.00298 ( 45) SS BOND : angle 1.14369 ( 90) hydrogen bonds : bond 0.03563 ( 1114) hydrogen bonds : angle 5.60027 ( 3111) link_ALPHA1-4 : bond 0.01736 ( 21) link_ALPHA1-4 : angle 2.98533 ( 63) link_BETA1-4 : bond 0.00441 ( 33) link_BETA1-4 : angle 1.56631 ( 99) link_BETA1-6 : bond 0.01941 ( 3) link_BETA1-6 : angle 2.55239 ( 9) link_NAG-ASN : bond 0.00385 ( 56) link_NAG-ASN : angle 2.88500 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6642 Ramachandran restraints generated. 3321 Oldfield, 0 Emsley, 3321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 484 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8941 (mt) cc_final: 0.8614 (mp) REVERT: A 140 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8015 (p90) REVERT: A 190 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7302 (mtt180) REVERT: A 207 HIS cc_start: 0.7536 (m170) cc_final: 0.7059 (m-70) REVERT: A 281 GLU cc_start: 0.8430 (pp20) cc_final: 0.8168 (pp20) REVERT: A 406 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 574 ASP cc_start: 0.8510 (t70) cc_final: 0.8003 (t0) REVERT: A 740 MET cc_start: 0.8992 (ttm) cc_final: 0.8718 (ttm) REVERT: A 773 GLU cc_start: 0.8574 (tp30) cc_final: 0.8045 (tt0) REVERT: A 780 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8364 (mt-10) REVERT: A 796 ASP cc_start: 0.8513 (t0) cc_final: 0.8235 (t0) REVERT: A 820 ASP cc_start: 0.8616 (m-30) cc_final: 0.8317 (m-30) REVERT: A 979 ASP cc_start: 0.8661 (t0) cc_final: 0.8410 (t0) REVERT: A 1019 ARG cc_start: 0.8419 (ttp-110) cc_final: 0.7850 (ttp-110) REVERT: A 1146 ASP cc_start: 0.7744 (m-30) cc_final: 0.7469 (m-30) REVERT: B 140 PHE cc_start: 0.8726 (p90) cc_final: 0.8357 (p90) REVERT: B 145 TYR cc_start: 0.5002 (OUTLIER) cc_final: 0.2388 (p90) REVERT: B 190 ARG cc_start: 0.8513 (tpp-160) cc_final: 0.7641 (mmt180) REVERT: B 314 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8234 (tm-30) REVERT: B 390 LEU cc_start: 0.8797 (mt) cc_final: 0.8444 (mt) REVERT: B 414 GLN cc_start: 0.8255 (mp10) cc_final: 0.7819 (mp10) REVERT: B 441 LEU cc_start: 0.8952 (mm) cc_final: 0.8751 (tt) REVERT: B 615 VAL cc_start: 0.9245 (t) cc_final: 0.8837 (m) REVERT: B 633 TRP cc_start: 0.8551 (p-90) cc_final: 0.8309 (p-90) REVERT: B 735 SER cc_start: 0.8787 (t) cc_final: 0.8553 (t) REVERT: B 738 CYS cc_start: 0.7501 (t) cc_final: 0.7137 (t) REVERT: B 786 LYS cc_start: 0.8354 (mmmt) cc_final: 0.8150 (mmmt) REVERT: B 804 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8220 (mm-40) REVERT: B 823 PHE cc_start: 0.8020 (m-80) cc_final: 0.7503 (m-80) REVERT: B 867 ASP cc_start: 0.8449 (m-30) cc_final: 0.8110 (m-30) REVERT: B 933 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8590 (mtpp) REVERT: B 979 ASP cc_start: 0.8659 (t0) cc_final: 0.8416 (t0) REVERT: B 1072 GLU cc_start: 0.8829 (pm20) cc_final: 0.8590 (pm20) REVERT: C 100 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8680 (mp) REVERT: C 121 ASN cc_start: 0.6842 (t0) cc_final: 0.6396 (t0) REVERT: C 177 MET cc_start: 0.3636 (mpp) cc_final: 0.3060 (mpp) REVERT: C 191 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7770 (mt-10) REVERT: C 354 ASN cc_start: 0.8516 (t0) cc_final: 0.8218 (t0) REVERT: C 571 ASP cc_start: 0.8316 (t0) cc_final: 0.7988 (t70) REVERT: C 633 TRP cc_start: 0.8711 (p-90) cc_final: 0.8310 (p-90) REVERT: C 737 ASP cc_start: 0.8457 (t0) cc_final: 0.8125 (t0) REVERT: C 790 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8447 (mmtm) REVERT: C 796 ASP cc_start: 0.8261 (t0) cc_final: 0.7751 (p0) REVERT: C 804 GLN cc_start: 0.8864 (mm110) cc_final: 0.8560 (mm-40) REVERT: C 883 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.8974 (p) REVERT: C 935 GLN cc_start: 0.8412 (tt0) cc_final: 0.7942 (tt0) REVERT: C 1125 ASN cc_start: 0.8765 (p0) cc_final: 0.7520 (p0) REVERT: C 1127 ASP cc_start: 0.8609 (m-30) cc_final: 0.8361 (p0) REVERT: C 1149 LYS cc_start: 0.8632 (tmtt) cc_final: 0.7947 (mttt) outliers start: 56 outliers final: 47 residues processed: 516 average time/residue: 0.1794 time to fit residues: 147.8613 Evaluate side-chains 521 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 470 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 331 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 312 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 321 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1119 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.103819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083214 restraints weight = 60239.064| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.30 r_work: 0.3098 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28490 Z= 0.159 Angle : 0.727 13.589 38970 Z= 0.347 Chirality : 0.045 0.493 4679 Planarity : 0.004 0.063 4827 Dihedral : 6.364 83.268 5942 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.12 % Favored : 94.79 % Rotamer: Outliers : 1.96 % Allowed : 16.92 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3321 helix: 1.96 (0.20), residues: 732 sheet: 0.18 (0.20), residues: 657 loop : -1.11 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 567 TYR 0.024 0.001 TYR B 473 PHE 0.028 0.001 PHE C 220 TRP 0.007 0.001 TRP C 152 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00358 (28332) covalent geometry : angle 0.69223 (38541) SS BOND : bond 0.00377 ( 45) SS BOND : angle 1.12569 ( 90) hydrogen bonds : bond 0.03638 ( 1114) hydrogen bonds : angle 5.60457 ( 3111) link_ALPHA1-4 : bond 0.01715 ( 21) link_ALPHA1-4 : angle 2.94042 ( 63) link_BETA1-4 : bond 0.00291 ( 33) link_BETA1-4 : angle 1.44005 ( 99) link_BETA1-6 : bond 0.02163 ( 3) link_BETA1-6 : angle 2.36127 ( 9) link_NAG-ASN : bond 0.00353 ( 56) link_NAG-ASN : angle 2.71074 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.52 seconds wall clock time: 111 minutes 46.01 seconds (6706.01 seconds total)