Starting phenix.real_space_refine on Tue Jun 24 06:41:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnw_26021/06_2025/7tnw_26021_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnw_26021/06_2025/7tnw_26021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnw_26021/06_2025/7tnw_26021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnw_26021/06_2025/7tnw_26021.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnw_26021/06_2025/7tnw_26021_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnw_26021/06_2025/7tnw_26021_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.038 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 17712 2.51 5 N 4485 2.21 5 O 5529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27846 Number of models: 1 Model: "" Number of chains: 39 Chain: "C" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 3 Chain: "A" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 3 Chain: "B" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} 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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 17.44, per 1000 atoms: 0.63 Number of scatterers: 27846 At special positions: 0 Unit cell: (148.57, 143.59, 196.71, 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 5529 8.00 N 4485 7.00 C 17712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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 A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1158 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1158 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1158 " " NAG D 1 " - " ASN C 17 " " NAG E 1 " - " ASN C 122 " " NAG F 1 " - " ASN C 165 " " NAG G 1 " - " ASN C 234 " " NAG H 1 " - " ASN C 282 " " NAG I 1 " - " ASN C 616 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1074 " " NAG M 1 " - " ASN C1098 " " NAG N 1 " - " ASN C1134 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN A 122 " " NAG Q 1 " - " ASN A 165 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 282 " " NAG T 1 " - " ASN A 616 " " NAG U 1 " - " ASN A 717 " " NAG V 1 " - " ASN A 801 " " NAG W 1 " - " ASN A1074 " " NAG X 1 " - " ASN A1098 " " NAG Y 1 " - " ASN A1134 " " NAG Z 1 " - " ASN B 17 " " NAG a 1 " - " ASN B 122 " " NAG b 1 " - " ASN B 165 " " NAG c 1 " - " ASN B 234 " " NAG d 1 " - " ASN B 282 " " NAG e 1 " - " ASN B 616 " " NAG f 1 " - " ASN B 717 " " NAG g 1 " - " ASN B 801 " " NAG h 1 " - " ASN B1074 " " NAG i 1 " - " ASN B1098 " " NAG j 1 " - " ASN B1134 " Time building additional restraints: 7.40 Conformation dependent library (CDL) restraints added in 3.1 seconds 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 48 sheets defined 27.6% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.773A 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: 4.173A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.534A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.847A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 639 removed outlier: 3.665A pdb=" N TYR C 636 " --> pdb=" O TRP C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.948A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.518A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 4.060A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 847 removed outlier: 4.170A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.850A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.665A 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: 3.502A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.547A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.313A 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 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.814A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1142 through 1160 removed outlier: 4.372A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.773A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.173A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.534A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.846A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.666A pdb=" N TYR A 636 " --> pdb=" O TRP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 3.948A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.518A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 4.061A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 847 removed outlier: 4.169A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.850A 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: 3.665A 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: 3.501A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.547A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.313A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.815A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1142 through 1160 removed outlier: 4.372A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.773A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.173A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.534A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.846A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.665A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.949A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.518A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.060A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 847 removed outlier: 4.169A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.850A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.664A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.502A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.547A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.313A 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 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.814A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1142 through 1160 removed outlier: 4.372A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.616A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.342A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.949A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.918A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.363A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.778A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.387A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 144 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.211A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.164A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.157A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.993A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.110A 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: 6.727A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 704 removed outlier: 6.690A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LYS A 790 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.044A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.956A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.280A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 787 through 790 removed outlier: 3.748A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.428A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.616A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.949A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.918A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.363A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.778A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.388A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.827A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A 144 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.211A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.164A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.158A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.993A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.681A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.044A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.956A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.281A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.427A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.616A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.949A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.918A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.363A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.778A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.387A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE B 144 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.211A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.158A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.993A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.044A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.956A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.280A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.428A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1117 hydrogen bonds defined for protein. 3000 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.64 Time building geometry restraints manager: 8.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4683 1.31 - 1.44: 7457 1.44 - 1.57: 16174 1.57 - 1.69: 3 1.69 - 1.82: 150 Bond restraints: 28467 Sorted by residual: bond pdb=" C ARG C 995 " pdb=" O ARG C 995 " ideal model delta sigma weight residual 1.236 1.185 0.052 1.16e-02 7.43e+03 2.00e+01 bond pdb=" C ARG A 995 " pdb=" O ARG A 995 " ideal model delta sigma weight residual 1.236 1.185 0.052 1.16e-02 7.43e+03 2.00e+01 bond pdb=" C ARG B 995 " pdb=" O ARG B 995 " ideal model delta sigma weight residual 1.236 1.185 0.052 1.16e-02 7.43e+03 1.99e+01 bond pdb=" CA ARG C1014 " pdb=" CB ARG C1014 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.58e-02 4.01e+03 1.91e+01 bond pdb=" CA ARG B1014 " pdb=" CB ARG B1014 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.58e-02 4.01e+03 1.89e+01 ... (remaining 28462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 29864 2.11 - 4.21: 7825 4.21 - 6.32: 917 6.32 - 8.43: 93 8.43 - 10.53: 10 Bond angle restraints: 38709 Sorted by residual: angle pdb=" N ARG A1091 " pdb=" CA ARG A1091 " pdb=" C ARG A1091 " ideal model delta sigma weight residual 111.03 103.07 7.96 1.11e+00 8.12e-01 5.14e+01 angle pdb=" N ARG C1091 " pdb=" CA ARG C1091 " pdb=" C ARG C1091 " ideal model delta sigma weight residual 111.03 103.09 7.94 1.11e+00 8.12e-01 5.12e+01 angle pdb=" N ARG B1091 " pdb=" CA ARG B1091 " pdb=" C ARG B1091 " ideal model delta sigma weight residual 111.03 103.12 7.91 1.11e+00 8.12e-01 5.08e+01 angle pdb=" CA ASN A 422 " pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 112.60 119.57 -6.97 1.00e+00 1.00e+00 4.86e+01 angle pdb=" CA ASN B 422 " pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 112.60 119.57 -6.97 1.00e+00 1.00e+00 4.86e+01 ... (remaining 38704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 17415 24.55 - 49.11: 708 49.11 - 73.66: 198 73.66 - 98.21: 45 98.21 - 122.76: 63 Dihedral angle restraints: 18429 sinusoidal: 8625 harmonic: 9804 Sorted by residual: dihedral pdb=" N ASN C 331 " pdb=" C ASN C 331 " pdb=" CA ASN C 331 " pdb=" CB ASN C 331 " ideal model delta harmonic sigma weight residual 122.80 144.17 -21.37 0 2.50e+00 1.60e-01 7.30e+01 dihedral pdb=" N ASN A 331 " pdb=" C ASN A 331 " pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " ideal model delta harmonic sigma weight residual 122.80 144.16 -21.36 0 2.50e+00 1.60e-01 7.30e+01 dihedral pdb=" N ASN B 331 " pdb=" C ASN B 331 " pdb=" CA ASN B 331 " pdb=" CB ASN B 331 " ideal model delta harmonic sigma weight residual 122.80 144.10 -21.30 0 2.50e+00 1.60e-01 7.26e+01 ... (remaining 18426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.325: 4653 0.325 - 0.649: 21 0.649 - 0.974: 6 0.974 - 1.298: 3 1.298 - 1.623: 12 Chirality restraints: 4695 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.80e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.66e+01 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.78 -1.62 2.00e-01 2.50e+01 6.58e+01 ... (remaining 4692 not shown) Planarity restraints: 4896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.142 2.00e-02 2.50e+03 1.17e-01 1.71e+02 pdb=" C7 NAG a 2 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.187 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " -0.142 2.00e-02 2.50e+03 1.17e-01 1.70e+02 pdb=" C7 NAG P 2 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " 0.187 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.141 2.00e-02 2.50e+03 1.17e-01 1.70e+02 pdb=" C7 NAG E 2 " 0.039 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.186 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 4893 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 873 2.74 - 3.28: 28092 3.28 - 3.82: 41990 3.82 - 4.36: 56723 4.36 - 4.90: 90540 Nonbonded interactions: 218218 Sorted by model distance: nonbonded pdb=" CZ PHE C 592 " pdb=" CE MET A 740 " model vdw 2.197 3.760 nonbonded pdb=" CE MET C 740 " pdb=" CZ PHE B 592 " model vdw 2.206 3.760 nonbonded pdb=" O MET A 900 " pdb=" CD2 TYR A 904 " model vdw 2.379 3.340 nonbonded pdb=" O MET B 900 " pdb=" CD2 TYR B 904 " model vdw 2.380 3.340 nonbonded pdb=" O MET C 900 " pdb=" CD2 TYR C 904 " model vdw 2.380 3.340 ... (remaining 218213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain '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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 66.140 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 0.014 0.080 28623 Z= 0.779 Angle : 2.023 45.200 39132 Z= 1.219 Chirality : 0.133 1.623 4695 Planarity : 0.013 0.117 4842 Dihedral : 16.814 122.764 11982 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.65 % Favored : 91.54 % Rotamer: Outliers : 1.81 % Allowed : 6.13 % Favored : 92.06 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 3333 helix: -1.43 (0.16), residues: 783 sheet: 0.35 (0.19), residues: 606 loop : -1.55 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.023 TRP B 64 HIS 0.011 0.003 HIS A 625 PHE 0.089 0.014 PHE A 133 TYR 0.110 0.018 TYR A 636 ARG 0.006 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.01620 ( 54) link_NAG-ASN : angle 13.62453 ( 162) link_ALPHA1-4 : bond 0.02567 ( 21) link_ALPHA1-4 : angle 3.26194 ( 63) link_BETA1-4 : bond 0.01584 ( 33) link_BETA1-4 : angle 3.05429 ( 99) hydrogen bonds : bond 0.16875 ( 1099) hydrogen bonds : angle 8.22778 ( 3000) link_BETA1-6 : bond 0.03072 ( 3) link_BETA1-6 : angle 2.65838 ( 9) SS BOND : bond 0.00996 ( 45) SS BOND : angle 2.17396 ( 90) covalent geometry : bond 0.01394 (28467) covalent geometry : angle 1.81788 (38709) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 668 time to evaluate : 3.488 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: C 41 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8353 (mmmm) REVERT: C 99 ASN cc_start: 0.7751 (t0) cc_final: 0.7307 (t0) REVERT: C 102 ARG cc_start: 0.7538 (mtt-85) cc_final: 0.6967 (mtt-85) REVERT: C 116 SER cc_start: 0.8734 (p) cc_final: 0.8412 (t) REVERT: C 140 PHE cc_start: 0.7981 (p90) cc_final: 0.7698 (p90) REVERT: C 176 LEU cc_start: 0.7516 (tp) cc_final: 0.7211 (tt) REVERT: C 191 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7825 (mt-10) REVERT: C 306 PHE cc_start: 0.8873 (m-80) cc_final: 0.8626 (m-80) REVERT: C 314 GLN cc_start: 0.8159 (mm110) cc_final: 0.7836 (mm-40) REVERT: C 317 ASN cc_start: 0.8376 (m110) cc_final: 0.6929 (m110) REVERT: C 351 TYR cc_start: 0.8217 (p90) cc_final: 0.7972 (p90) REVERT: C 393 THR cc_start: 0.7521 (m) cc_final: 0.7319 (p) REVERT: C 586 ASP cc_start: 0.8209 (m-30) cc_final: 0.7838 (m-30) REVERT: C 654 GLU cc_start: 0.7814 (tt0) cc_final: 0.7389 (tt0) REVERT: C 675 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7355 (pp30) REVERT: C 690 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7733 (mm-40) REVERT: C 693 ILE cc_start: 0.9342 (pt) cc_final: 0.9040 (pt) REVERT: C 755 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8342 (mp10) REVERT: C 773 GLU cc_start: 0.8140 (tp30) cc_final: 0.7924 (tt0) REVERT: C 776 LYS cc_start: 0.8836 (tttp) cc_final: 0.8518 (tttm) REVERT: C 780 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 790 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8690 (mtpp) REVERT: C 814 LYS cc_start: 0.8781 (mptt) cc_final: 0.8540 (mttm) REVERT: C 837 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.6087 (t80) REVERT: C 849 LEU cc_start: 0.8531 (tp) cc_final: 0.8260 (tt) REVERT: C 987 VAL cc_start: 0.8965 (t) cc_final: 0.8080 (t) REVERT: C 1125 ASN cc_start: 0.8525 (p0) cc_final: 0.8148 (p0) REVERT: A 116 SER cc_start: 0.8672 (p) cc_final: 0.8448 (t) REVERT: A 140 PHE cc_start: 0.8128 (p90) cc_final: 0.7844 (p90) REVERT: A 190 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7540 (mtm-85) REVERT: A 191 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7764 (mt-10) REVERT: A 287 ASP cc_start: 0.8497 (t0) cc_final: 0.8230 (t0) REVERT: A 314 GLN cc_start: 0.8287 (mm110) cc_final: 0.7881 (mm-40) REVERT: A 317 ASN cc_start: 0.8349 (m110) cc_final: 0.6945 (m110) REVERT: A 353 TRP cc_start: 0.8382 (p-90) cc_final: 0.8149 (p-90) REVERT: A 564 GLN cc_start: 0.7896 (tp40) cc_final: 0.7692 (tp-100) REVERT: A 581 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 586 ASP cc_start: 0.8315 (m-30) cc_final: 0.7972 (m-30) REVERT: A 615 VAL cc_start: 0.8660 (t) cc_final: 0.8206 (p) REVERT: A 632 THR cc_start: 0.8514 (m) cc_final: 0.8270 (p) REVERT: A 654 GLU cc_start: 0.7629 (tt0) cc_final: 0.7313 (tt0) REVERT: A 675 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7277 (pp30) REVERT: A 737 ASP cc_start: 0.7853 (t0) cc_final: 0.7527 (t0) REVERT: A 740 MET cc_start: 0.8457 (ttp) cc_final: 0.8236 (ttm) REVERT: A 755 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8367 (mp10) REVERT: A 765 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.8274 (ttp80) REVERT: A 773 GLU cc_start: 0.8166 (tp30) cc_final: 0.7916 (tt0) REVERT: A 780 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8259 (mt-10) REVERT: A 790 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8568 (mtpp) REVERT: A 837 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.6085 (t80) REVERT: A 1005 GLN cc_start: 0.8602 (tp40) cc_final: 0.8049 (tp40) REVERT: A 1125 ASN cc_start: 0.8542 (p0) cc_final: 0.8144 (p0) REVERT: B 153 MET cc_start: 0.5896 (tmm) cc_final: 0.5577 (tmm) REVERT: B 191 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 239 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7443 (tm-30) REVERT: B 287 ASP cc_start: 0.8582 (t0) cc_final: 0.8342 (t0) REVERT: B 314 GLN cc_start: 0.8346 (mm110) cc_final: 0.7896 (mm-40) REVERT: B 317 ASN cc_start: 0.8418 (m110) cc_final: 0.7363 (m-40) REVERT: B 353 TRP cc_start: 0.8383 (p-90) cc_final: 0.7852 (p-90) REVERT: B 393 THR cc_start: 0.7619 (m) cc_final: 0.7395 (p) REVERT: B 400 PHE cc_start: 0.7528 (p90) cc_final: 0.7302 (p90) REVERT: B 402 ILE cc_start: 0.8416 (pt) cc_final: 0.8155 (pt) REVERT: B 557 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8746 (mtmt) REVERT: B 581 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8105 (p) REVERT: B 615 VAL cc_start: 0.8698 (t) cc_final: 0.8224 (p) REVERT: B 654 GLU cc_start: 0.7816 (tt0) cc_final: 0.7612 (tt0) REVERT: B 661 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7945 (mm-30) REVERT: B 737 ASP cc_start: 0.7726 (t0) cc_final: 0.7432 (t0) REVERT: B 765 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.8157 (ttm-80) REVERT: B 790 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8486 (mtpp) REVERT: B 804 GLN cc_start: 0.7964 (mt0) cc_final: 0.7758 (mt0) REVERT: B 811 LYS cc_start: 0.8259 (ttmm) cc_final: 0.7746 (tttp) REVERT: B 814 LYS cc_start: 0.8789 (mptt) cc_final: 0.8573 (mptt) REVERT: B 820 ASP cc_start: 0.8282 (t70) cc_final: 0.8037 (t0) REVERT: B 837 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.6114 (t80) outliers start: 53 outliers final: 10 residues processed: 707 average time/residue: 0.4384 time to fit residues: 476.3830 Evaluate side-chains 527 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 510 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 837 TYR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 837 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.4980 chunk 252 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 170 optimal weight: 0.0050 chunk 134 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 302 optimal weight: 0.9980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C 417 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 836 GLN A 121 ASN A 394 ASN A 417 ASN A 613 GLN A 836 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN B 481 ASN B 519 HIS B 613 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.109699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.087315 restraints weight = 61556.084| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.53 r_work: 0.3203 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28623 Z= 0.175 Angle : 0.903 18.324 39132 Z= 0.427 Chirality : 0.056 0.748 4695 Planarity : 0.004 0.044 4842 Dihedral : 14.236 112.555 5920 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.79 % Allowed : 9.75 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3333 helix: 0.74 (0.19), residues: 750 sheet: 0.26 (0.19), residues: 663 loop : -1.25 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 64 HIS 0.005 0.001 HIS B 519 PHE 0.023 0.002 PHE A1148 TYR 0.020 0.002 TYR C 265 ARG 0.009 0.001 ARG B 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 54) link_NAG-ASN : angle 5.40734 ( 162) link_ALPHA1-4 : bond 0.01469 ( 21) link_ALPHA1-4 : angle 2.41621 ( 63) link_BETA1-4 : bond 0.00364 ( 33) link_BETA1-4 : angle 2.01909 ( 99) hydrogen bonds : bond 0.05073 ( 1099) hydrogen bonds : angle 6.21447 ( 3000) link_BETA1-6 : bond 0.01551 ( 3) link_BETA1-6 : angle 1.70131 ( 9) SS BOND : bond 0.00994 ( 45) SS BOND : angle 3.05511 ( 90) covalent geometry : bond 0.00385 (28467) covalent geometry : angle 0.81195 (38709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 541 time to evaluate : 2.731 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: C 41 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8366 (mmmm) REVERT: C 95 ILE cc_start: 0.9046 (tp) cc_final: 0.8845 (tp) REVERT: C 99 ASN cc_start: 0.8285 (t0) cc_final: 0.7778 (t0) REVERT: C 102 ARG cc_start: 0.8073 (mtt-85) cc_final: 0.7543 (mtt-85) REVERT: C 121 ASN cc_start: 0.6630 (t0) cc_final: 0.6369 (t0) REVERT: C 140 PHE cc_start: 0.7998 (p90) cc_final: 0.7791 (p90) REVERT: C 191 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7960 (mt-10) REVERT: C 239 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7555 (tm-30) REVERT: C 287 ASP cc_start: 0.8455 (t0) cc_final: 0.8107 (t0) REVERT: C 306 PHE cc_start: 0.8969 (m-80) cc_final: 0.8630 (m-80) REVERT: C 317 ASN cc_start: 0.8409 (m110) cc_final: 0.7905 (m-40) REVERT: C 586 ASP cc_start: 0.8196 (m-30) cc_final: 0.7779 (m-30) REVERT: C 654 GLU cc_start: 0.8290 (tt0) cc_final: 0.7937 (tt0) REVERT: C 675 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7274 (pp30) REVERT: C 690 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7581 (mm-40) REVERT: C 693 ILE cc_start: 0.9408 (pt) cc_final: 0.9074 (pt) REVERT: C 776 LYS cc_start: 0.9004 (tttp) cc_final: 0.8786 (ttpp) REVERT: C 790 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8772 (mtpp) REVERT: C 811 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8116 (ttmm) REVERT: C 950 ASP cc_start: 0.8298 (m-30) cc_final: 0.7937 (m-30) REVERT: C 1125 ASN cc_start: 0.8554 (p0) cc_final: 0.8209 (p0) REVERT: C 1148 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6789 (p90) REVERT: A 41 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8506 (mmmm) REVERT: A 51 THR cc_start: 0.8868 (t) cc_final: 0.8664 (p) REVERT: A 137 ASN cc_start: 0.8688 (t0) cc_final: 0.8413 (p0) REVERT: A 191 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7787 (mt-10) REVERT: A 239 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 287 ASP cc_start: 0.8520 (t0) cc_final: 0.8273 (t0) REVERT: A 317 ASN cc_start: 0.8259 (m110) cc_final: 0.7754 (m-40) REVERT: A 380 TYR cc_start: 0.7991 (m-80) cc_final: 0.7120 (m-80) REVERT: A 577 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8204 (ttm170) REVERT: A 581 THR cc_start: 0.8718 (p) cc_final: 0.8386 (p) REVERT: A 586 ASP cc_start: 0.8305 (m-30) cc_final: 0.7974 (m-30) REVERT: A 632 THR cc_start: 0.8397 (m) cc_final: 0.8036 (p) REVERT: A 654 GLU cc_start: 0.8260 (tt0) cc_final: 0.7882 (tt0) REVERT: A 675 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7303 (pp30) REVERT: A 693 ILE cc_start: 0.9366 (pt) cc_final: 0.9145 (pt) REVERT: A 755 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8576 (mm-40) REVERT: A 773 GLU cc_start: 0.8309 (tp30) cc_final: 0.8108 (tt0) REVERT: A 776 LYS cc_start: 0.9046 (tttp) cc_final: 0.8782 (tttp) REVERT: A 780 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 790 LYS cc_start: 0.9000 (mtmt) cc_final: 0.8728 (mtpp) REVERT: A 820 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: A 1005 GLN cc_start: 0.8592 (tp40) cc_final: 0.8150 (tp40) REVERT: A 1125 ASN cc_start: 0.8601 (p0) cc_final: 0.7509 (p0) REVERT: B 41 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8415 (mmmm) REVERT: B 99 ASN cc_start: 0.8115 (t0) cc_final: 0.7880 (t0) REVERT: B 105 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8496 (mt) REVERT: B 121 ASN cc_start: 0.6434 (t0) cc_final: 0.6193 (t0) REVERT: B 153 MET cc_start: 0.6045 (tmm) cc_final: 0.5607 (tmm) REVERT: B 191 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7811 (mt-10) REVERT: B 218 GLN cc_start: 0.8652 (tt0) cc_final: 0.8263 (mt0) REVERT: B 287 ASP cc_start: 0.8633 (t0) cc_final: 0.8419 (t0) REVERT: B 323 THR cc_start: 0.8560 (p) cc_final: 0.8264 (p) REVERT: B 338 PHE cc_start: 0.7231 (m-80) cc_final: 0.6838 (m-80) REVERT: B 355 ARG cc_start: 0.8184 (ttt90) cc_final: 0.7765 (ttt90) REVERT: B 369 TYR cc_start: 0.7167 (t80) cc_final: 0.6899 (t80) REVERT: B 466 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6182 (ptp90) REVERT: B 557 LYS cc_start: 0.9055 (mtmm) cc_final: 0.8832 (mtmt) REVERT: B 581 THR cc_start: 0.8536 (p) cc_final: 0.8255 (p) REVERT: B 615 VAL cc_start: 0.8810 (t) cc_final: 0.8602 (p) REVERT: B 646 ARG cc_start: 0.8927 (tpp80) cc_final: 0.8682 (mmm160) REVERT: B 649 CYS cc_start: 0.7537 (t) cc_final: 0.7140 (t) REVERT: B 762 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7886 (mm-40) REVERT: B 790 LYS cc_start: 0.8960 (mtmt) cc_final: 0.8655 (mtpp) REVERT: B 957 GLN cc_start: 0.8504 (tt0) cc_final: 0.8235 (tm-30) REVERT: B 964 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8747 (mtmm) REVERT: B 995 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7823 (mtt-85) outliers start: 82 outliers final: 39 residues processed: 586 average time/residue: 0.4159 time to fit residues: 375.5892 Evaluate side-chains 507 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 460 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1152 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 127 optimal weight: 4.9990 chunk 291 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 204 optimal weight: 0.3980 chunk 183 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 303 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN C 271 GLN C 450 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 218 GLN A 314 GLN A 417 ASN A 564 GLN A 613 GLN B 30 ASN B 137 ASN B 314 GLN B 317 ASN B 450 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.107723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085702 restraints weight = 61516.260| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.48 r_work: 0.3178 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 28623 Z= 0.189 Angle : 0.827 15.463 39132 Z= 0.388 Chirality : 0.052 0.620 4695 Planarity : 0.004 0.045 4842 Dihedral : 13.266 109.269 5901 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.24 % Allowed : 11.52 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3333 helix: 1.13 (0.19), residues: 765 sheet: 0.22 (0.19), residues: 708 loop : -1.23 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 436 HIS 0.004 0.001 HIS C1064 PHE 0.021 0.002 PHE A 168 TYR 0.021 0.002 TYR C1067 ARG 0.004 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 54) link_NAG-ASN : angle 4.55706 ( 162) link_ALPHA1-4 : bond 0.01602 ( 21) link_ALPHA1-4 : angle 2.54189 ( 63) link_BETA1-4 : bond 0.00263 ( 33) link_BETA1-4 : angle 1.69462 ( 99) hydrogen bonds : bond 0.04572 ( 1099) hydrogen bonds : angle 5.86486 ( 3000) link_BETA1-6 : bond 0.01382 ( 3) link_BETA1-6 : angle 1.92537 ( 9) SS BOND : bond 0.00352 ( 45) SS BOND : angle 2.14564 ( 90) covalent geometry : bond 0.00436 (28467) covalent geometry : angle 0.75851 (38709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 504 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8285 (mmmm) REVERT: C 99 ASN cc_start: 0.8320 (t0) cc_final: 0.8023 (t0) REVERT: C 102 ARG cc_start: 0.8037 (mtt-85) cc_final: 0.7569 (mmt90) REVERT: C 121 ASN cc_start: 0.6485 (t0) cc_final: 0.6139 (t0) REVERT: C 191 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8051 (mt-10) REVERT: C 239 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7686 (tm-30) REVERT: C 287 ASP cc_start: 0.8479 (t0) cc_final: 0.8123 (t0) REVERT: C 306 PHE cc_start: 0.9011 (m-80) cc_final: 0.8629 (m-80) REVERT: C 317 ASN cc_start: 0.8239 (m110) cc_final: 0.8004 (m110) REVERT: C 398 ASP cc_start: 0.7193 (m-30) cc_final: 0.6691 (t0) REVERT: C 434 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7087 (tt) REVERT: C 586 ASP cc_start: 0.8213 (m-30) cc_final: 0.7811 (m-30) REVERT: C 654 GLU cc_start: 0.8284 (tt0) cc_final: 0.7895 (tt0) REVERT: C 675 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7275 (pp30) REVERT: C 690 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7679 (mm-40) REVERT: C 693 ILE cc_start: 0.9399 (pt) cc_final: 0.9091 (pt) REVERT: C 776 LYS cc_start: 0.8951 (tttp) cc_final: 0.8717 (ttpp) REVERT: C 780 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8301 (mt-10) REVERT: C 790 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8718 (mtpp) REVERT: C 811 LYS cc_start: 0.8467 (ttmm) cc_final: 0.7838 (ttmm) REVERT: C 820 ASP cc_start: 0.8537 (t0) cc_final: 0.8186 (m-30) REVERT: C 950 ASP cc_start: 0.8329 (m-30) cc_final: 0.7933 (m-30) REVERT: C 1072 GLU cc_start: 0.8818 (pm20) cc_final: 0.8579 (pm20) REVERT: C 1125 ASN cc_start: 0.8565 (p0) cc_final: 0.8171 (p0) REVERT: C 1148 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6314 (p90) REVERT: A 41 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8424 (mmmm) REVERT: A 116 SER cc_start: 0.8759 (m) cc_final: 0.8496 (p) REVERT: A 191 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 239 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 287 ASP cc_start: 0.8530 (t0) cc_final: 0.8293 (t0) REVERT: A 581 THR cc_start: 0.8718 (p) cc_final: 0.7555 (p) REVERT: A 586 ASP cc_start: 0.8359 (m-30) cc_final: 0.7898 (m-30) REVERT: A 632 THR cc_start: 0.8403 (m) cc_final: 0.8002 (p) REVERT: A 654 GLU cc_start: 0.8304 (tt0) cc_final: 0.7929 (tt0) REVERT: A 675 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7301 (pp30) REVERT: A 693 ILE cc_start: 0.9380 (pt) cc_final: 0.9106 (pt) REVERT: A 755 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8575 (mm-40) REVERT: A 773 GLU cc_start: 0.8340 (tp30) cc_final: 0.8115 (tt0) REVERT: A 776 LYS cc_start: 0.8994 (tttp) cc_final: 0.8709 (tttp) REVERT: A 780 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8108 (mt-10) REVERT: A 790 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8733 (mtpp) REVERT: A 820 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: A 950 ASP cc_start: 0.8229 (m-30) cc_final: 0.7871 (m-30) REVERT: A 1005 GLN cc_start: 0.8638 (tp40) cc_final: 0.8291 (tp40) REVERT: A 1072 GLU cc_start: 0.8725 (pm20) cc_final: 0.8325 (pm20) REVERT: A 1125 ASN cc_start: 0.8636 (p0) cc_final: 0.8172 (p0) REVERT: A 1127 ASP cc_start: 0.8316 (p0) cc_final: 0.8085 (p0) REVERT: B 41 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8354 (mmmm) REVERT: B 99 ASN cc_start: 0.8120 (t0) cc_final: 0.7918 (t0) REVERT: B 129 LYS cc_start: 0.8064 (tttt) cc_final: 0.7680 (ptmm) REVERT: B 153 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5444 (tmm) REVERT: B 186 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: B 190 ARG cc_start: 0.8409 (mtt90) cc_final: 0.8155 (mtt90) REVERT: B 191 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7720 (mt-10) REVERT: B 323 THR cc_start: 0.8780 (p) cc_final: 0.8580 (p) REVERT: B 355 ARG cc_start: 0.8334 (ttt90) cc_final: 0.7866 (ttt90) REVERT: B 369 TYR cc_start: 0.7252 (t80) cc_final: 0.6974 (t80) REVERT: B 422 ASN cc_start: 0.6190 (p0) cc_final: 0.4619 (p0) REVERT: B 557 LYS cc_start: 0.9096 (mtmm) cc_final: 0.8854 (mtmt) REVERT: B 581 THR cc_start: 0.8557 (p) cc_final: 0.8259 (p) REVERT: B 646 ARG cc_start: 0.8991 (tpp80) cc_final: 0.8720 (mmm160) REVERT: B 762 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7870 (mm-40) REVERT: B 790 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8625 (mtpp) REVERT: B 811 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8167 (ttmm) REVERT: B 820 ASP cc_start: 0.8612 (t0) cc_final: 0.8285 (m-30) REVERT: B 964 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8803 (mtmm) REVERT: B 995 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7834 (mtt-85) REVERT: B 1107 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8541 (mtt180) outliers start: 95 outliers final: 51 residues processed: 552 average time/residue: 0.4166 time to fit residues: 357.6008 Evaluate side-chains 525 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 466 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1152 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 102 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 94 optimal weight: 0.4980 chunk 324 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN A 121 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 613 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 137 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.109091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086691 restraints weight = 61979.917| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.54 r_work: 0.3213 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 28623 Z= 0.149 Angle : 0.797 14.013 39132 Z= 0.372 Chirality : 0.050 0.542 4695 Planarity : 0.004 0.044 4842 Dihedral : 12.648 107.306 5897 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.45 % Allowed : 13.63 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3333 helix: 1.26 (0.20), residues: 774 sheet: 0.45 (0.19), residues: 648 loop : -1.11 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 436 HIS 0.002 0.001 HIS C1159 PHE 0.038 0.002 PHE C 338 TYR 0.020 0.001 TYR A 421 ARG 0.006 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 54) link_NAG-ASN : angle 3.98518 ( 162) link_ALPHA1-4 : bond 0.01548 ( 21) link_ALPHA1-4 : angle 2.62495 ( 63) link_BETA1-4 : bond 0.00289 ( 33) link_BETA1-4 : angle 1.61515 ( 99) hydrogen bonds : bond 0.04041 ( 1099) hydrogen bonds : angle 5.77440 ( 3000) link_BETA1-6 : bond 0.01410 ( 3) link_BETA1-6 : angle 2.12126 ( 9) SS BOND : bond 0.00439 ( 45) SS BOND : angle 2.58066 ( 90) covalent geometry : bond 0.00336 (28467) covalent geometry : angle 0.73590 (38709) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 502 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8337 (mmmm) REVERT: C 99 ASN cc_start: 0.8389 (t0) cc_final: 0.8140 (t0) REVERT: C 102 ARG cc_start: 0.8048 (mtt-85) cc_final: 0.7657 (mmt90) REVERT: C 121 ASN cc_start: 0.6408 (t0) cc_final: 0.6124 (t0) REVERT: C 129 LYS cc_start: 0.8007 (tttt) cc_final: 0.7738 (ptmm) REVERT: C 191 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8054 (mt-10) REVERT: C 287 ASP cc_start: 0.8498 (t0) cc_final: 0.8289 (t0) REVERT: C 317 ASN cc_start: 0.8230 (m110) cc_final: 0.7950 (m110) REVERT: C 398 ASP cc_start: 0.7187 (m-30) cc_final: 0.6657 (t0) REVERT: C 563 GLN cc_start: 0.7973 (mt0) cc_final: 0.7645 (mp10) REVERT: C 586 ASP cc_start: 0.8206 (m-30) cc_final: 0.7783 (m-30) REVERT: C 649 CYS cc_start: 0.7201 (t) cc_final: 0.6883 (t) REVERT: C 654 GLU cc_start: 0.8355 (tt0) cc_final: 0.7955 (tt0) REVERT: C 675 GLN cc_start: 0.7725 (pt0) cc_final: 0.7279 (pp30) REVERT: C 690 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7713 (mm-40) REVERT: C 693 ILE cc_start: 0.9391 (pt) cc_final: 0.9076 (pt) REVERT: C 776 LYS cc_start: 0.8921 (tttp) cc_final: 0.8678 (ttpp) REVERT: C 780 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8257 (mt-10) REVERT: C 790 LYS cc_start: 0.8948 (mtmt) cc_final: 0.8658 (mtpp) REVERT: C 811 LYS cc_start: 0.8442 (ttmm) cc_final: 0.7901 (ttmm) REVERT: C 820 ASP cc_start: 0.8521 (t0) cc_final: 0.8149 (m-30) REVERT: C 977 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8077 (mp) REVERT: C 1072 GLU cc_start: 0.8796 (pm20) cc_final: 0.8531 (pm20) REVERT: C 1125 ASN cc_start: 0.8517 (p0) cc_final: 0.8116 (p0) REVERT: C 1148 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.6249 (p90) REVERT: A 41 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8385 (mmmm) REVERT: A 116 SER cc_start: 0.8724 (m) cc_final: 0.8430 (p) REVERT: A 129 LYS cc_start: 0.8097 (tttt) cc_final: 0.7752 (ptmm) REVERT: A 190 ARG cc_start: 0.8517 (mtt90) cc_final: 0.7963 (mtt90) REVERT: A 191 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7826 (mt-10) REVERT: A 581 THR cc_start: 0.8418 (p) cc_final: 0.8113 (p) REVERT: A 586 ASP cc_start: 0.8338 (m-30) cc_final: 0.7903 (m-30) REVERT: A 632 THR cc_start: 0.8380 (m) cc_final: 0.7929 (p) REVERT: A 654 GLU cc_start: 0.8361 (tt0) cc_final: 0.7967 (tt0) REVERT: A 755 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8577 (mm-40) REVERT: A 773 GLU cc_start: 0.8255 (tp30) cc_final: 0.8022 (tt0) REVERT: A 776 LYS cc_start: 0.8918 (tttp) cc_final: 0.8658 (tttp) REVERT: A 790 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8736 (mtpp) REVERT: A 814 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8633 (mmtm) REVERT: A 820 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8113 (m-30) REVERT: A 950 ASP cc_start: 0.8199 (m-30) cc_final: 0.7786 (m-30) REVERT: A 1005 GLN cc_start: 0.8601 (tp40) cc_final: 0.8287 (tp40) REVERT: A 1072 GLU cc_start: 0.8687 (pm20) cc_final: 0.8252 (pm20) REVERT: A 1125 ASN cc_start: 0.8670 (p0) cc_final: 0.8297 (p0) REVERT: A 1127 ASP cc_start: 0.8357 (p0) cc_final: 0.8141 (p0) REVERT: B 41 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8293 (mmmm) REVERT: B 80 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6901 (p0) REVERT: B 95 ILE cc_start: 0.9106 (mm) cc_final: 0.8714 (tp) REVERT: B 99 ASN cc_start: 0.8203 (t0) cc_final: 0.7976 (t0) REVERT: B 129 LYS cc_start: 0.8053 (tttt) cc_final: 0.7822 (ptmm) REVERT: B 153 MET cc_start: 0.5975 (OUTLIER) cc_final: 0.5409 (tmm) REVERT: B 186 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6178 (m-80) REVERT: B 191 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 355 ARG cc_start: 0.8295 (ttt90) cc_final: 0.7853 (ttt90) REVERT: B 369 TYR cc_start: 0.7262 (t80) cc_final: 0.7043 (t80) REVERT: B 422 ASN cc_start: 0.6174 (p0) cc_final: 0.4613 (p0) REVERT: B 466 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6544 (ptp90) REVERT: B 516 GLU cc_start: 0.7243 (tp30) cc_final: 0.7005 (tp30) REVERT: B 557 LYS cc_start: 0.9089 (mtmm) cc_final: 0.8786 (mtmt) REVERT: B 581 THR cc_start: 0.8611 (p) cc_final: 0.8313 (p) REVERT: B 586 ASP cc_start: 0.8237 (m-30) cc_final: 0.7974 (m-30) REVERT: B 592 PHE cc_start: 0.8376 (p90) cc_final: 0.8169 (p90) REVERT: B 646 ARG cc_start: 0.8994 (tpp80) cc_final: 0.8721 (mmm160) REVERT: B 737 ASP cc_start: 0.7592 (t0) cc_final: 0.7384 (t0) REVERT: B 762 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7794 (mm-40) REVERT: B 790 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8585 (mtpp) REVERT: B 811 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8171 (ttmm) REVERT: B 820 ASP cc_start: 0.8571 (t0) cc_final: 0.8214 (m-30) REVERT: B 995 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7840 (mtt-85) outliers start: 72 outliers final: 39 residues processed: 539 average time/residue: 0.4295 time to fit residues: 356.7369 Evaluate side-chains 521 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 475 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 316 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 321 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 186 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 314 GLN A 354 ASN A1011 GLN B 121 ASN B 314 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.107967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085740 restraints weight = 61824.797| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.51 r_work: 0.3177 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 28623 Z= 0.171 Angle : 0.783 13.875 39132 Z= 0.363 Chirality : 0.049 0.506 4695 Planarity : 0.004 0.044 4842 Dihedral : 12.022 106.310 5887 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.14 % Allowed : 13.60 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3333 helix: 1.39 (0.20), residues: 765 sheet: 0.40 (0.20), residues: 591 loop : -1.10 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 PHE 0.024 0.002 PHE C 32 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 54) link_NAG-ASN : angle 3.68361 ( 162) link_ALPHA1-4 : bond 0.01702 ( 21) link_ALPHA1-4 : angle 2.86129 ( 63) link_BETA1-4 : bond 0.00251 ( 33) link_BETA1-4 : angle 1.56441 ( 99) hydrogen bonds : bond 0.03991 ( 1099) hydrogen bonds : angle 5.66277 ( 3000) link_BETA1-6 : bond 0.01422 ( 3) link_BETA1-6 : angle 2.29928 ( 9) SS BOND : bond 0.00509 ( 45) SS BOND : angle 2.38949 ( 90) covalent geometry : bond 0.00392 (28467) covalent geometry : angle 0.72780 (38709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 501 time to evaluate : 3.247 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: C 41 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8394 (mmtp) REVERT: C 102 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7656 (mmt90) REVERT: C 121 ASN cc_start: 0.6428 (t0) cc_final: 0.6203 (t0) REVERT: C 129 LYS cc_start: 0.7987 (tttt) cc_final: 0.7740 (ptmm) REVERT: C 191 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7999 (mt-10) REVERT: C 239 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7752 (tm-30) REVERT: C 317 ASN cc_start: 0.8203 (m110) cc_final: 0.7967 (m110) REVERT: C 377 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.6431 (t80) REVERT: C 390 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8782 (mp) REVERT: C 398 ASP cc_start: 0.7089 (m-30) cc_final: 0.6564 (t0) REVERT: C 434 ILE cc_start: 0.7397 (mp) cc_final: 0.7080 (mt) REVERT: C 465 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6999 (tp30) REVERT: C 558 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8647 (mmmm) REVERT: C 563 GLN cc_start: 0.7999 (mt0) cc_final: 0.7686 (mp10) REVERT: C 586 ASP cc_start: 0.8212 (m-30) cc_final: 0.7806 (m-30) REVERT: C 649 CYS cc_start: 0.7149 (t) cc_final: 0.6713 (t) REVERT: C 654 GLU cc_start: 0.8348 (tt0) cc_final: 0.7930 (tt0) REVERT: C 675 GLN cc_start: 0.7760 (pt0) cc_final: 0.7307 (pp30) REVERT: C 690 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7785 (mm-40) REVERT: C 693 ILE cc_start: 0.9401 (pt) cc_final: 0.9120 (pt) REVERT: C 762 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7805 (mm110) REVERT: C 776 LYS cc_start: 0.8949 (tttp) cc_final: 0.8707 (ttpp) REVERT: C 780 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8256 (mt-10) REVERT: C 790 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8640 (mtpp) REVERT: C 811 LYS cc_start: 0.8457 (ttmm) cc_final: 0.7872 (ttmm) REVERT: C 820 ASP cc_start: 0.8537 (t0) cc_final: 0.8164 (m-30) REVERT: C 977 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8105 (mp) REVERT: C 1072 GLU cc_start: 0.8841 (pm20) cc_final: 0.8592 (pm20) REVERT: C 1148 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6417 (p90) REVERT: A 41 LYS cc_start: 0.8723 (mmmm) cc_final: 0.8433 (mmmm) REVERT: A 116 SER cc_start: 0.8731 (m) cc_final: 0.8435 (p) REVERT: A 129 LYS cc_start: 0.8063 (tttt) cc_final: 0.7685 (pttt) REVERT: A 135 PHE cc_start: 0.7527 (m-80) cc_final: 0.7198 (m-80) REVERT: A 190 ARG cc_start: 0.8343 (mtt90) cc_final: 0.7941 (mtt90) REVERT: A 191 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 287 ASP cc_start: 0.8485 (t0) cc_final: 0.8241 (t0) REVERT: A 377 PHE cc_start: 0.6826 (OUTLIER) cc_final: 0.6500 (t80) REVERT: A 571 ASP cc_start: 0.8537 (t0) cc_final: 0.8278 (t0) REVERT: A 581 THR cc_start: 0.8426 (p) cc_final: 0.8089 (p) REVERT: A 586 ASP cc_start: 0.8306 (m-30) cc_final: 0.7943 (m-30) REVERT: A 654 GLU cc_start: 0.8430 (tt0) cc_final: 0.8034 (tt0) REVERT: A 755 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8477 (mp10) REVERT: A 776 LYS cc_start: 0.8951 (tttp) cc_final: 0.8678 (tttp) REVERT: A 790 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8758 (mtpp) REVERT: A 820 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: A 950 ASP cc_start: 0.8250 (m-30) cc_final: 0.7801 (m-30) REVERT: A 1005 GLN cc_start: 0.8642 (tp40) cc_final: 0.8343 (tp40) REVERT: A 1072 GLU cc_start: 0.8724 (pm20) cc_final: 0.8269 (pm20) REVERT: A 1125 ASN cc_start: 0.8684 (p0) cc_final: 0.8367 (p0) REVERT: B 41 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8311 (mmmm) REVERT: B 95 ILE cc_start: 0.9053 (mm) cc_final: 0.8771 (tp) REVERT: B 99 ASN cc_start: 0.8293 (t0) cc_final: 0.7194 (t0) REVERT: B 102 ARG cc_start: 0.7745 (mtt-85) cc_final: 0.6975 (mmt90) REVERT: B 129 LYS cc_start: 0.8099 (tttt) cc_final: 0.7772 (ptmm) REVERT: B 153 MET cc_start: 0.5962 (OUTLIER) cc_final: 0.5381 (tmm) REVERT: B 191 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 239 GLN cc_start: 0.7830 (tp40) cc_final: 0.7615 (tp40) REVERT: B 355 ARG cc_start: 0.8389 (ttt90) cc_final: 0.7938 (ttt90) REVERT: B 377 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6369 (t80) REVERT: B 390 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8723 (mp) REVERT: B 400 PHE cc_start: 0.7429 (p90) cc_final: 0.7050 (p90) REVERT: B 466 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6510 (ptp90) REVERT: B 557 LYS cc_start: 0.9074 (mtmm) cc_final: 0.8765 (mtmt) REVERT: B 581 THR cc_start: 0.8648 (p) cc_final: 0.8360 (p) REVERT: B 586 ASP cc_start: 0.8254 (m-30) cc_final: 0.7906 (m-30) REVERT: B 592 PHE cc_start: 0.8311 (p90) cc_final: 0.8013 (p90) REVERT: B 646 ARG cc_start: 0.9047 (tpp80) cc_final: 0.8745 (mmm160) REVERT: B 740 MET cc_start: 0.8802 (tpp) cc_final: 0.8405 (tpp) REVERT: B 762 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7797 (mm110) REVERT: B 773 GLU cc_start: 0.7811 (tt0) cc_final: 0.7597 (tt0) REVERT: B 790 LYS cc_start: 0.8912 (mtmt) cc_final: 0.8591 (mtpp) REVERT: B 811 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8102 (ttmm) REVERT: B 820 ASP cc_start: 0.8578 (t0) cc_final: 0.8224 (m-30) REVERT: B 995 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7830 (mtt-85) outliers start: 92 outliers final: 59 residues processed: 546 average time/residue: 0.4654 time to fit residues: 396.4435 Evaluate side-chains 539 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 470 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 266 optimal weight: 5.9990 chunk 326 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 294 optimal weight: 2.9990 chunk 256 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 237 optimal weight: 0.2980 chunk 37 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN C 66 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN A 66 HIS A 314 GLN A 354 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.108510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086097 restraints weight = 61857.040| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.57 r_work: 0.3180 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 0.080 28623 Z= 0.153 Angle : 0.777 13.255 39132 Z= 0.361 Chirality : 0.049 0.483 4695 Planarity : 0.004 0.042 4842 Dihedral : 11.597 105.693 5886 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.93 % Allowed : 15.44 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3333 helix: 1.35 (0.20), residues: 777 sheet: 0.45 (0.19), residues: 642 loop : -1.07 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS C1064 PHE 0.018 0.001 PHE B 32 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 54) link_NAG-ASN : angle 3.52402 ( 162) link_ALPHA1-4 : bond 0.01632 ( 21) link_ALPHA1-4 : angle 2.95158 ( 63) link_BETA1-4 : bond 0.00285 ( 33) link_BETA1-4 : angle 1.51314 ( 99) hydrogen bonds : bond 0.03830 ( 1099) hydrogen bonds : angle 5.59496 ( 3000) link_BETA1-6 : bond 0.01369 ( 3) link_BETA1-6 : angle 2.35199 ( 9) SS BOND : bond 0.00655 ( 45) SS BOND : angle 2.57523 ( 90) covalent geometry : bond 0.00349 (28467) covalent geometry : angle 0.72206 (38709) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 489 time to evaluate : 3.084 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: C 41 LYS cc_start: 0.8732 (mmmm) cc_final: 0.8293 (mmmm) REVERT: C 102 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7710 (mmt90) REVERT: C 129 LYS cc_start: 0.7962 (tttt) cc_final: 0.7724 (ptmm) REVERT: C 191 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7972 (mt-10) REVERT: C 237 ARG cc_start: 0.8363 (mtp-110) cc_final: 0.8147 (mtp85) REVERT: C 239 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7830 (tm-30) REVERT: C 317 ASN cc_start: 0.8334 (m110) cc_final: 0.8119 (m110) REVERT: C 351 TYR cc_start: 0.8494 (p90) cc_final: 0.7938 (p90) REVERT: C 377 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6436 (t80) REVERT: C 390 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8792 (mp) REVERT: C 398 ASP cc_start: 0.7097 (m-30) cc_final: 0.6533 (t0) REVERT: C 434 ILE cc_start: 0.7426 (mp) cc_final: 0.7117 (mt) REVERT: C 563 GLN cc_start: 0.8020 (mt0) cc_final: 0.7661 (mp10) REVERT: C 586 ASP cc_start: 0.8232 (m-30) cc_final: 0.7786 (m-30) REVERT: C 649 CYS cc_start: 0.7177 (t) cc_final: 0.6741 (t) REVERT: C 654 GLU cc_start: 0.8397 (tt0) cc_final: 0.8007 (tt0) REVERT: C 675 GLN cc_start: 0.7804 (pt0) cc_final: 0.7601 (pp30) REVERT: C 693 ILE cc_start: 0.9391 (pt) cc_final: 0.9118 (pt) REVERT: C 762 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7682 (mm110) REVERT: C 776 LYS cc_start: 0.8903 (tttp) cc_final: 0.8663 (ttpp) REVERT: C 780 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8319 (mt-10) REVERT: C 790 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8677 (mtpp) REVERT: C 814 LYS cc_start: 0.8684 (mptt) cc_final: 0.8317 (mmtt) REVERT: C 820 ASP cc_start: 0.8515 (t0) cc_final: 0.8127 (m-30) REVERT: C 977 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8153 (mp) REVERT: C 1072 GLU cc_start: 0.8864 (pm20) cc_final: 0.8593 (pm20) REVERT: C 1148 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.6308 (p90) REVERT: A 41 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8430 (mmmm) REVERT: A 100 ILE cc_start: 0.9120 (mp) cc_final: 0.8855 (mp) REVERT: A 116 SER cc_start: 0.8710 (m) cc_final: 0.8377 (p) REVERT: A 129 LYS cc_start: 0.8080 (tttt) cc_final: 0.7755 (ptmm) REVERT: A 186 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6252 (m-80) REVERT: A 190 ARG cc_start: 0.8379 (mtt90) cc_final: 0.7973 (mtt90) REVERT: A 191 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 239 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 287 ASP cc_start: 0.8490 (t0) cc_final: 0.8224 (t0) REVERT: A 377 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6497 (t80) REVERT: A 571 ASP cc_start: 0.8610 (t0) cc_final: 0.8353 (t0) REVERT: A 581 THR cc_start: 0.8446 (p) cc_final: 0.8112 (p) REVERT: A 586 ASP cc_start: 0.8334 (m-30) cc_final: 0.7927 (m-30) REVERT: A 654 GLU cc_start: 0.8438 (tt0) cc_final: 0.8013 (tt0) REVERT: A 675 GLN cc_start: 0.7477 (pp30) cc_final: 0.7054 (pp30) REVERT: A 755 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8501 (mp10) REVERT: A 776 LYS cc_start: 0.8927 (tttp) cc_final: 0.8682 (tttp) REVERT: A 790 LYS cc_start: 0.9006 (mtmt) cc_final: 0.8755 (mtpp) REVERT: A 820 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: A 950 ASP cc_start: 0.8298 (m-30) cc_final: 0.7827 (m-30) REVERT: A 1005 GLN cc_start: 0.8631 (tp40) cc_final: 0.8328 (tp40) REVERT: A 1072 GLU cc_start: 0.8730 (pm20) cc_final: 0.8242 (pm20) REVERT: B 41 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8289 (mmmm) REVERT: B 95 ILE cc_start: 0.9048 (mm) cc_final: 0.8760 (tp) REVERT: B 99 ASN cc_start: 0.8354 (t0) cc_final: 0.7788 (t0) REVERT: B 102 ARG cc_start: 0.7809 (mtt-85) cc_final: 0.7585 (mtt90) REVERT: B 129 LYS cc_start: 0.8162 (tttt) cc_final: 0.7807 (ptmm) REVERT: B 153 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.5373 (tmm) REVERT: B 191 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7833 (mt-10) REVERT: B 355 ARG cc_start: 0.8341 (ttt90) cc_final: 0.7902 (ttt90) REVERT: B 377 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.6062 (t80) REVERT: B 390 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8746 (mp) REVERT: B 400 PHE cc_start: 0.7486 (p90) cc_final: 0.7044 (p90) REVERT: B 466 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6513 (ptp90) REVERT: B 516 GLU cc_start: 0.7146 (tp30) cc_final: 0.6935 (tp30) REVERT: B 547 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8278 (mtpp) REVERT: B 557 LYS cc_start: 0.9090 (mtmm) cc_final: 0.8758 (mtmt) REVERT: B 581 THR cc_start: 0.8665 (p) cc_final: 0.8376 (p) REVERT: B 586 ASP cc_start: 0.8269 (m-30) cc_final: 0.7885 (m-30) REVERT: B 592 PHE cc_start: 0.8218 (p90) cc_final: 0.7964 (p90) REVERT: B 646 ARG cc_start: 0.9018 (tpp80) cc_final: 0.8646 (mmm160) REVERT: B 740 MET cc_start: 0.8716 (tpp) cc_final: 0.8418 (tpp) REVERT: B 762 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7763 (mm110) REVERT: B 773 GLU cc_start: 0.7816 (tt0) cc_final: 0.7592 (tt0) REVERT: B 790 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8583 (mtpp) REVERT: B 995 ARG cc_start: 0.8214 (mtt-85) cc_final: 0.7840 (mtt-85) REVERT: B 1144 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8381 (mm-30) outliers start: 86 outliers final: 52 residues processed: 536 average time/residue: 0.4260 time to fit residues: 354.9901 Evaluate side-chains 533 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 470 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 325 optimal weight: 0.6980 chunk 317 optimal weight: 0.6980 chunk 222 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 214 optimal weight: 0.0040 chunk 79 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 121 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 613 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1125 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.108169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086191 restraints weight = 61597.106| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.47 r_work: 0.3190 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28623 Z= 0.153 Angle : 0.770 12.992 39132 Z= 0.357 Chirality : 0.049 0.490 4695 Planarity : 0.004 0.040 4842 Dihedral : 11.171 104.925 5886 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.86 % Allowed : 16.16 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3333 helix: 1.39 (0.20), residues: 777 sheet: 0.50 (0.19), residues: 642 loop : -1.06 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.003 0.001 HIS C1064 PHE 0.024 0.001 PHE C 338 TYR 0.019 0.001 TYR C 380 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 54) link_NAG-ASN : angle 3.38348 ( 162) link_ALPHA1-4 : bond 0.01674 ( 21) link_ALPHA1-4 : angle 2.91724 ( 63) link_BETA1-4 : bond 0.00271 ( 33) link_BETA1-4 : angle 1.46508 ( 99) hydrogen bonds : bond 0.03741 ( 1099) hydrogen bonds : angle 5.52030 ( 3000) link_BETA1-6 : bond 0.01404 ( 3) link_BETA1-6 : angle 2.46850 ( 9) SS BOND : bond 0.00540 ( 45) SS BOND : angle 2.42135 ( 90) covalent geometry : bond 0.00352 (28467) covalent geometry : angle 0.71901 (38709) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 496 time to evaluate : 2.830 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: C 41 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8284 (mmmm) REVERT: C 121 ASN cc_start: 0.6843 (OUTLIER) cc_final: 0.6604 (t0) REVERT: C 191 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7969 (mt-10) REVERT: C 239 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7846 (tm-30) REVERT: C 317 ASN cc_start: 0.8309 (m110) cc_final: 0.8100 (m110) REVERT: C 377 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.6419 (t80) REVERT: C 390 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8765 (mp) REVERT: C 398 ASP cc_start: 0.7028 (m-30) cc_final: 0.6518 (t0) REVERT: C 434 ILE cc_start: 0.7389 (mp) cc_final: 0.7069 (mt) REVERT: C 563 GLN cc_start: 0.8018 (mt0) cc_final: 0.7682 (mp10) REVERT: C 586 ASP cc_start: 0.8192 (m-30) cc_final: 0.7760 (m-30) REVERT: C 649 CYS cc_start: 0.7092 (t) cc_final: 0.6679 (t) REVERT: C 654 GLU cc_start: 0.8355 (tt0) cc_final: 0.7959 (tt0) REVERT: C 762 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7647 (mm110) REVERT: C 776 LYS cc_start: 0.8897 (tttp) cc_final: 0.8663 (ttpp) REVERT: C 780 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8279 (mt-10) REVERT: C 790 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8657 (mtpp) REVERT: C 811 LYS cc_start: 0.8459 (ttmm) cc_final: 0.7898 (ttmm) REVERT: C 814 LYS cc_start: 0.8664 (mptt) cc_final: 0.8275 (mmtt) REVERT: C 820 ASP cc_start: 0.8502 (t0) cc_final: 0.8116 (m-30) REVERT: C 977 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8193 (mp) REVERT: C 1072 GLU cc_start: 0.8864 (pm20) cc_final: 0.8604 (pm20) REVERT: A 41 LYS cc_start: 0.8744 (mmmm) cc_final: 0.8504 (mmmm) REVERT: A 95 ILE cc_start: 0.9072 (tt) cc_final: 0.8682 (tp) REVERT: A 100 ILE cc_start: 0.9069 (mp) cc_final: 0.8812 (mp) REVERT: A 116 SER cc_start: 0.8720 (m) cc_final: 0.8398 (p) REVERT: A 129 LYS cc_start: 0.8043 (tttt) cc_final: 0.7723 (ptmm) REVERT: A 186 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: A 191 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 239 GLN cc_start: 0.8293 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 287 ASP cc_start: 0.8460 (t0) cc_final: 0.8189 (t0) REVERT: A 377 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6486 (t80) REVERT: A 571 ASP cc_start: 0.8590 (t0) cc_final: 0.8341 (t0) REVERT: A 581 THR cc_start: 0.8446 (p) cc_final: 0.8188 (p) REVERT: A 586 ASP cc_start: 0.8294 (m-30) cc_final: 0.7896 (m-30) REVERT: A 654 GLU cc_start: 0.8405 (tt0) cc_final: 0.8002 (tt0) REVERT: A 675 GLN cc_start: 0.7474 (pp30) cc_final: 0.7034 (pp30) REVERT: A 755 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8467 (mp10) REVERT: A 776 LYS cc_start: 0.8902 (tttp) cc_final: 0.8657 (tttp) REVERT: A 790 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8732 (mtpp) REVERT: A 820 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: A 950 ASP cc_start: 0.8268 (m-30) cc_final: 0.7788 (m-30) REVERT: A 1072 GLU cc_start: 0.8727 (pm20) cc_final: 0.8212 (pm20) REVERT: B 41 LYS cc_start: 0.8673 (mmmm) cc_final: 0.8352 (mmmm) REVERT: B 95 ILE cc_start: 0.9046 (mm) cc_final: 0.8781 (tp) REVERT: B 99 ASN cc_start: 0.8319 (t0) cc_final: 0.8071 (t0) REVERT: B 102 ARG cc_start: 0.7769 (mtt-85) cc_final: 0.7381 (mmt90) REVERT: B 121 ASN cc_start: 0.6896 (OUTLIER) cc_final: 0.6444 (t0) REVERT: B 129 LYS cc_start: 0.8126 (tttt) cc_final: 0.7788 (ptmm) REVERT: B 153 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5369 (tmm) REVERT: B 191 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7828 (mt-10) REVERT: B 332 ILE cc_start: 0.8189 (mm) cc_final: 0.7901 (mt) REVERT: B 355 ARG cc_start: 0.8425 (ttt90) cc_final: 0.7869 (ttt90) REVERT: B 377 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.6239 (t80) REVERT: B 390 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8691 (mp) REVERT: B 400 PHE cc_start: 0.7474 (p90) cc_final: 0.7023 (p90) REVERT: B 466 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6520 (ptp90) REVERT: B 557 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8741 (mtmt) REVERT: B 563 GLN cc_start: 0.8068 (mt0) cc_final: 0.7800 (mp10) REVERT: B 571 ASP cc_start: 0.8513 (t0) cc_final: 0.8005 (t0) REVERT: B 581 THR cc_start: 0.8669 (p) cc_final: 0.8382 (p) REVERT: B 586 ASP cc_start: 0.8250 (m-30) cc_final: 0.7855 (m-30) REVERT: B 592 PHE cc_start: 0.8159 (p90) cc_final: 0.7930 (p90) REVERT: B 646 ARG cc_start: 0.9000 (tpp80) cc_final: 0.8595 (mmm160) REVERT: B 762 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7682 (mm-40) REVERT: B 773 GLU cc_start: 0.7795 (tt0) cc_final: 0.7568 (tt0) REVERT: B 790 LYS cc_start: 0.8895 (mtmt) cc_final: 0.8562 (mtpp) REVERT: B 811 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7852 (ttmm) REVERT: B 814 LYS cc_start: 0.8872 (mptt) cc_final: 0.8475 (mmtt) REVERT: B 820 ASP cc_start: 0.8547 (t0) cc_final: 0.8181 (m-30) REVERT: B 995 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7800 (mtt-85) outliers start: 84 outliers final: 65 residues processed: 543 average time/residue: 0.4120 time to fit residues: 345.8104 Evaluate side-chains 555 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 478 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 119 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 325 optimal weight: 0.5980 chunk 225 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1011 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 613 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.106774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084626 restraints weight = 62115.241| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.50 r_work: 0.3158 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 28623 Z= 0.218 Angle : 0.812 13.583 39132 Z= 0.379 Chirality : 0.050 0.495 4695 Planarity : 0.004 0.041 4842 Dihedral : 10.995 104.848 5886 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.00 % Allowed : 16.53 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3333 helix: 1.43 (0.20), residues: 777 sheet: 0.45 (0.20), residues: 618 loop : -1.11 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.006 0.001 HIS A 519 PHE 0.015 0.002 PHE B 140 TYR 0.020 0.002 TYR C 380 ARG 0.008 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 54) link_NAG-ASN : angle 3.48565 ( 162) link_ALPHA1-4 : bond 0.01734 ( 21) link_ALPHA1-4 : angle 2.98042 ( 63) link_BETA1-4 : bond 0.00206 ( 33) link_BETA1-4 : angle 1.51475 ( 99) hydrogen bonds : bond 0.04024 ( 1099) hydrogen bonds : angle 5.53963 ( 3000) link_BETA1-6 : bond 0.01405 ( 3) link_BETA1-6 : angle 2.66881 ( 9) SS BOND : bond 0.00610 ( 45) SS BOND : angle 2.44070 ( 90) covalent geometry : bond 0.00508 (28467) covalent geometry : angle 0.76195 (38709) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 497 time to evaluate : 2.767 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: C 41 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8341 (mmmm) REVERT: C 137 ASN cc_start: 0.8889 (m110) cc_final: 0.8687 (m-40) REVERT: C 187 LYS cc_start: 0.8727 (tptt) cc_final: 0.8525 (tptt) REVERT: C 191 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7984 (mt-10) REVERT: C 317 ASN cc_start: 0.8256 (m110) cc_final: 0.8034 (m110) REVERT: C 351 TYR cc_start: 0.8546 (p90) cc_final: 0.8193 (p90) REVERT: C 377 PHE cc_start: 0.6829 (OUTLIER) cc_final: 0.6481 (t80) REVERT: C 390 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8832 (mp) REVERT: C 398 ASP cc_start: 0.7041 (m-30) cc_final: 0.6527 (t0) REVERT: C 434 ILE cc_start: 0.7413 (mp) cc_final: 0.7116 (mt) REVERT: C 563 GLN cc_start: 0.8069 (mt0) cc_final: 0.7691 (mp10) REVERT: C 586 ASP cc_start: 0.8205 (m-30) cc_final: 0.7824 (m-30) REVERT: C 633 TRP cc_start: 0.9242 (OUTLIER) cc_final: 0.9037 (p-90) REVERT: C 649 CYS cc_start: 0.7082 (t) cc_final: 0.6647 (t) REVERT: C 654 GLU cc_start: 0.8333 (tt0) cc_final: 0.7892 (tt0) REVERT: C 690 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7614 (mm-40) REVERT: C 762 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7703 (mm110) REVERT: C 776 LYS cc_start: 0.8904 (tttp) cc_final: 0.8674 (ttpp) REVERT: C 780 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8333 (mt-10) REVERT: C 811 LYS cc_start: 0.8476 (ttmm) cc_final: 0.7991 (ttmm) REVERT: C 820 ASP cc_start: 0.8525 (t0) cc_final: 0.8133 (m-30) REVERT: C 977 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8198 (mp) REVERT: C 1072 GLU cc_start: 0.8901 (pm20) cc_final: 0.8622 (pm20) REVERT: C 1148 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6034 (p90) REVERT: A 41 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8418 (mmmm) REVERT: A 100 ILE cc_start: 0.9172 (mp) cc_final: 0.8919 (mp) REVERT: A 116 SER cc_start: 0.8725 (m) cc_final: 0.8431 (p) REVERT: A 129 LYS cc_start: 0.8084 (tttt) cc_final: 0.7743 (ptmm) REVERT: A 137 ASN cc_start: 0.8524 (m110) cc_final: 0.8050 (p0) REVERT: A 191 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 239 GLN cc_start: 0.8270 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 287 ASP cc_start: 0.8485 (t0) cc_final: 0.8227 (t0) REVERT: A 377 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6618 (t80) REVERT: A 571 ASP cc_start: 0.8650 (t0) cc_final: 0.8425 (t0) REVERT: A 581 THR cc_start: 0.8423 (p) cc_final: 0.8168 (p) REVERT: A 586 ASP cc_start: 0.8293 (m-30) cc_final: 0.7901 (m-30) REVERT: A 654 GLU cc_start: 0.8419 (tt0) cc_final: 0.8024 (tt0) REVERT: A 675 GLN cc_start: 0.7476 (pp30) cc_final: 0.7040 (pp30) REVERT: A 755 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8506 (mp10) REVERT: A 776 LYS cc_start: 0.8921 (tttp) cc_final: 0.8668 (tttp) REVERT: A 790 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8738 (mtpp) REVERT: A 820 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: A 950 ASP cc_start: 0.8326 (m-30) cc_final: 0.7897 (m-30) REVERT: A 977 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 1072 GLU cc_start: 0.8769 (pm20) cc_final: 0.8247 (pm20) REVERT: B 41 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8318 (mmmm) REVERT: B 95 ILE cc_start: 0.9042 (mm) cc_final: 0.8673 (tp) REVERT: B 102 ARG cc_start: 0.7901 (mtt-85) cc_final: 0.7695 (mmt90) REVERT: B 129 LYS cc_start: 0.8133 (tttt) cc_final: 0.7795 (ptmm) REVERT: B 153 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5312 (tmm) REVERT: B 191 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 332 ILE cc_start: 0.8238 (mm) cc_final: 0.7947 (mt) REVERT: B 355 ARG cc_start: 0.8443 (ttt90) cc_final: 0.7958 (ttt90) REVERT: B 377 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6261 (t80) REVERT: B 390 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8712 (mp) REVERT: B 466 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6621 (ptp90) REVERT: B 516 GLU cc_start: 0.7167 (tp30) cc_final: 0.6929 (tp30) REVERT: B 557 LYS cc_start: 0.9043 (mtmm) cc_final: 0.8793 (mtmt) REVERT: B 571 ASP cc_start: 0.8541 (t0) cc_final: 0.8035 (t0) REVERT: B 586 ASP cc_start: 0.8207 (m-30) cc_final: 0.7900 (m-30) REVERT: B 646 ARG cc_start: 0.9014 (tpp80) cc_final: 0.8604 (mmm160) REVERT: B 740 MET cc_start: 0.8716 (tpp) cc_final: 0.8446 (tpp) REVERT: B 762 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7798 (mm110) REVERT: B 773 GLU cc_start: 0.7853 (tt0) cc_final: 0.7647 (tt0) REVERT: B 790 LYS cc_start: 0.8929 (mtmt) cc_final: 0.8697 (mmmm) REVERT: B 814 LYS cc_start: 0.8891 (mptt) cc_final: 0.8595 (mmtt) REVERT: B 995 ARG cc_start: 0.8272 (mtt-85) cc_final: 0.7900 (mtt-85) REVERT: B 1144 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8409 (mm-30) outliers start: 88 outliers final: 66 residues processed: 548 average time/residue: 0.4340 time to fit residues: 366.5671 Evaluate side-chains 555 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 477 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 277 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 311 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 112 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN C 121 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 613 GLN B 66 HIS B 121 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.107972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085654 restraints weight = 62147.121| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.57 r_work: 0.3173 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28623 Z= 0.159 Angle : 0.793 13.360 39132 Z= 0.370 Chirality : 0.049 0.482 4695 Planarity : 0.004 0.039 4842 Dihedral : 10.494 104.769 5886 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.83 % Allowed : 17.08 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3333 helix: 1.47 (0.20), residues: 777 sheet: 0.34 (0.19), residues: 672 loop : -1.05 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.006 0.001 HIS A 519 PHE 0.021 0.001 PHE C 338 TYR 0.018 0.001 TYR C1067 ARG 0.008 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 54) link_NAG-ASN : angle 3.26601 ( 162) link_ALPHA1-4 : bond 0.01720 ( 21) link_ALPHA1-4 : angle 2.92898 ( 63) link_BETA1-4 : bond 0.00262 ( 33) link_BETA1-4 : angle 1.43174 ( 99) hydrogen bonds : bond 0.03782 ( 1099) hydrogen bonds : angle 5.56209 ( 3000) link_BETA1-6 : bond 0.01499 ( 3) link_BETA1-6 : angle 2.68848 ( 9) SS BOND : bond 0.00475 ( 45) SS BOND : angle 2.45266 ( 90) covalent geometry : bond 0.00367 (28467) covalent geometry : angle 0.74625 (38709) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 501 time to evaluate : 2.958 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: C 41 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8362 (mmmm) REVERT: C 187 LYS cc_start: 0.8705 (tptt) cc_final: 0.8482 (tptt) REVERT: C 191 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8080 (mt-10) REVERT: C 317 ASN cc_start: 0.8352 (m110) cc_final: 0.8052 (m110) REVERT: C 351 TYR cc_start: 0.8550 (p90) cc_final: 0.8197 (p90) REVERT: C 377 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.6467 (t80) REVERT: C 390 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8812 (mp) REVERT: C 434 ILE cc_start: 0.7447 (mp) cc_final: 0.7156 (mt) REVERT: C 563 GLN cc_start: 0.7962 (mt0) cc_final: 0.7670 (mp10) REVERT: C 586 ASP cc_start: 0.8180 (m-30) cc_final: 0.7802 (m-30) REVERT: C 633 TRP cc_start: 0.9203 (OUTLIER) cc_final: 0.9001 (p-90) REVERT: C 649 CYS cc_start: 0.7063 (t) cc_final: 0.6632 (t) REVERT: C 654 GLU cc_start: 0.8370 (tt0) cc_final: 0.7950 (tt0) REVERT: C 690 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7499 (mm-40) REVERT: C 776 LYS cc_start: 0.8902 (tttp) cc_final: 0.8673 (ttpp) REVERT: C 780 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8330 (mt-10) REVERT: C 811 LYS cc_start: 0.8458 (ttmm) cc_final: 0.7974 (ttmm) REVERT: C 820 ASP cc_start: 0.8507 (t0) cc_final: 0.8119 (m-30) REVERT: C 977 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8181 (mp) REVERT: C 1072 GLU cc_start: 0.8873 (pm20) cc_final: 0.8606 (pm20) REVERT: A 100 ILE cc_start: 0.9135 (mp) cc_final: 0.8875 (mp) REVERT: A 116 SER cc_start: 0.8690 (m) cc_final: 0.8398 (p) REVERT: A 129 LYS cc_start: 0.8036 (tttt) cc_final: 0.7736 (ptmm) REVERT: A 137 ASN cc_start: 0.8495 (m110) cc_final: 0.8024 (p0) REVERT: A 186 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6310 (m-80) REVERT: A 191 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7840 (mt-10) REVERT: A 239 GLN cc_start: 0.8278 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 287 ASP cc_start: 0.8480 (t0) cc_final: 0.8220 (t0) REVERT: A 377 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6547 (t80) REVERT: A 571 ASP cc_start: 0.8646 (t0) cc_final: 0.8427 (t0) REVERT: A 581 THR cc_start: 0.8467 (p) cc_final: 0.8212 (p) REVERT: A 586 ASP cc_start: 0.8301 (m-30) cc_final: 0.7913 (m-30) REVERT: A 633 TRP cc_start: 0.9210 (OUTLIER) cc_final: 0.8899 (p-90) REVERT: A 646 ARG cc_start: 0.8820 (mmm-85) cc_final: 0.8502 (mmm160) REVERT: A 654 GLU cc_start: 0.8427 (tt0) cc_final: 0.8029 (tt0) REVERT: A 675 GLN cc_start: 0.7488 (pp30) cc_final: 0.7077 (pp30) REVERT: A 737 ASP cc_start: 0.7534 (t0) cc_final: 0.7227 (t0) REVERT: A 755 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8517 (mp10) REVERT: A 776 LYS cc_start: 0.8920 (tttp) cc_final: 0.8668 (tttp) REVERT: A 790 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8709 (mtpp) REVERT: A 820 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: A 950 ASP cc_start: 0.8309 (m-30) cc_final: 0.7834 (m-30) REVERT: A 977 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8439 (mp) REVERT: B 41 LYS cc_start: 0.8698 (mmmm) cc_final: 0.8278 (mmmm) REVERT: B 95 ILE cc_start: 0.9004 (mm) cc_final: 0.8671 (tp) REVERT: B 129 LYS cc_start: 0.8137 (tttt) cc_final: 0.7821 (ptmm) REVERT: B 153 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5289 (tmm) REVERT: B 190 ARG cc_start: 0.8425 (mtt90) cc_final: 0.7326 (mpt90) REVERT: B 191 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7760 (mt-10) REVERT: B 237 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8086 (mtp85) REVERT: B 332 ILE cc_start: 0.8217 (mm) cc_final: 0.7937 (mt) REVERT: B 355 ARG cc_start: 0.8435 (ttt90) cc_final: 0.7982 (ttt90) REVERT: B 377 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6237 (t80) REVERT: B 390 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8687 (mp) REVERT: B 466 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6534 (ptp90) REVERT: B 516 GLU cc_start: 0.7374 (tp30) cc_final: 0.7061 (tp30) REVERT: B 557 LYS cc_start: 0.9031 (mtmm) cc_final: 0.8781 (mtmt) REVERT: B 563 GLN cc_start: 0.8054 (mt0) cc_final: 0.7796 (mp10) REVERT: B 571 ASP cc_start: 0.8537 (t0) cc_final: 0.8022 (t0) REVERT: B 586 ASP cc_start: 0.8198 (m-30) cc_final: 0.7878 (m-30) REVERT: B 646 ARG cc_start: 0.8995 (tpp80) cc_final: 0.8461 (mmm160) REVERT: B 762 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7708 (mm-40) REVERT: B 773 GLU cc_start: 0.7820 (tt0) cc_final: 0.7617 (tt0) REVERT: B 790 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8743 (mtmm) REVERT: B 811 LYS cc_start: 0.8372 (ttmm) cc_final: 0.7742 (ttmm) REVERT: B 814 LYS cc_start: 0.8840 (mptt) cc_final: 0.8463 (mmtt) REVERT: B 820 ASP cc_start: 0.8584 (t0) cc_final: 0.8173 (m-30) REVERT: B 995 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7826 (mtt-85) REVERT: B 1144 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8368 (mm-30) outliers start: 83 outliers final: 60 residues processed: 551 average time/residue: 0.4236 time to fit residues: 361.8413 Evaluate side-chains 542 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 469 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 92 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 201 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN C 121 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 613 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.106872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084815 restraints weight = 62006.099| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.49 r_work: 0.3161 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 28623 Z= 0.208 Angle : 0.840 15.265 39132 Z= 0.393 Chirality : 0.050 0.488 4695 Planarity : 0.004 0.091 4842 Dihedral : 10.183 104.481 5886 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.69 % Allowed : 17.31 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3333 helix: 1.43 (0.20), residues: 777 sheet: 0.52 (0.19), residues: 630 loop : -1.13 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.005 0.001 HIS A 519 PHE 0.035 0.001 PHE C 133 TYR 0.035 0.002 TYR C 380 ARG 0.020 0.001 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 54) link_NAG-ASN : angle 3.35814 ( 162) link_ALPHA1-4 : bond 0.01858 ( 21) link_ALPHA1-4 : angle 3.04931 ( 63) link_BETA1-4 : bond 0.00242 ( 33) link_BETA1-4 : angle 1.48996 ( 99) hydrogen bonds : bond 0.03958 ( 1099) hydrogen bonds : angle 5.54543 ( 3000) link_BETA1-6 : bond 0.01598 ( 3) link_BETA1-6 : angle 2.77095 ( 9) SS BOND : bond 0.00743 ( 45) SS BOND : angle 2.97125 ( 90) covalent geometry : bond 0.00489 (28467) covalent geometry : angle 0.78935 (38709) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 484 time to evaluate : 3.248 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: C 41 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8392 (mmmm) REVERT: C 102 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7725 (mmt90) REVERT: C 191 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8034 (mt-10) REVERT: C 287 ASP cc_start: 0.8471 (t0) cc_final: 0.8239 (t0) REVERT: C 317 ASN cc_start: 0.8351 (m110) cc_final: 0.8101 (m110) REVERT: C 351 TYR cc_start: 0.8558 (p90) cc_final: 0.8217 (p90) REVERT: C 377 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.6213 (t80) REVERT: C 390 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8837 (mp) REVERT: C 434 ILE cc_start: 0.7451 (mp) cc_final: 0.7174 (mt) REVERT: C 586 ASP cc_start: 0.8194 (m-30) cc_final: 0.7831 (m-30) REVERT: C 633 TRP cc_start: 0.9162 (OUTLIER) cc_final: 0.8937 (p-90) REVERT: C 649 CYS cc_start: 0.7017 (t) cc_final: 0.6598 (t) REVERT: C 654 GLU cc_start: 0.8368 (tt0) cc_final: 0.7953 (tt0) REVERT: C 690 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7498 (mm-40) REVERT: C 762 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7728 (mm110) REVERT: C 776 LYS cc_start: 0.8929 (tttp) cc_final: 0.8713 (ttpp) REVERT: C 780 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8353 (mt-10) REVERT: C 811 LYS cc_start: 0.8438 (ttmm) cc_final: 0.7908 (ttmm) REVERT: C 820 ASP cc_start: 0.8522 (t0) cc_final: 0.8133 (m-30) REVERT: C 957 GLN cc_start: 0.8471 (tt0) cc_final: 0.8249 (tm-30) REVERT: C 977 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8204 (mp) REVERT: C 1072 GLU cc_start: 0.8876 (pm20) cc_final: 0.8604 (pm20) REVERT: A 100 ILE cc_start: 0.9158 (mp) cc_final: 0.8896 (mp) REVERT: A 116 SER cc_start: 0.8694 (m) cc_final: 0.8419 (p) REVERT: A 129 LYS cc_start: 0.8064 (tttt) cc_final: 0.7749 (ptmm) REVERT: A 137 ASN cc_start: 0.8497 (m110) cc_final: 0.8046 (p0) REVERT: A 186 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: A 191 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7836 (mt-10) REVERT: A 239 GLN cc_start: 0.8298 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 287 ASP cc_start: 0.8479 (t0) cc_final: 0.8217 (t0) REVERT: A 377 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.6394 (t80) REVERT: A 571 ASP cc_start: 0.8664 (t0) cc_final: 0.8452 (t0) REVERT: A 581 THR cc_start: 0.8453 (p) cc_final: 0.8200 (p) REVERT: A 586 ASP cc_start: 0.8277 (m-30) cc_final: 0.7998 (m-30) REVERT: A 646 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8486 (mmm160) REVERT: A 654 GLU cc_start: 0.8435 (tt0) cc_final: 0.8107 (tt0) REVERT: A 675 GLN cc_start: 0.7532 (pp30) cc_final: 0.7119 (pp30) REVERT: A 737 ASP cc_start: 0.7453 (t0) cc_final: 0.7114 (t0) REVERT: A 755 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8521 (mp10) REVERT: A 776 LYS cc_start: 0.8937 (tttp) cc_final: 0.8691 (tttp) REVERT: A 790 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8733 (mtpp) REVERT: A 820 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: A 950 ASP cc_start: 0.8344 (m-30) cc_final: 0.7887 (m-30) REVERT: A 977 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8447 (mp) REVERT: B 41 LYS cc_start: 0.8696 (mmmm) cc_final: 0.8307 (mmmm) REVERT: B 95 ILE cc_start: 0.8960 (mm) cc_final: 0.8707 (tp) REVERT: B 129 LYS cc_start: 0.8138 (tttt) cc_final: 0.7860 (ptmm) REVERT: B 153 MET cc_start: 0.5883 (OUTLIER) cc_final: 0.5316 (tmm) REVERT: B 190 ARG cc_start: 0.8432 (mtt90) cc_final: 0.7332 (mpt90) REVERT: B 191 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7744 (mt-10) REVERT: B 332 ILE cc_start: 0.8238 (mm) cc_final: 0.7967 (mt) REVERT: B 355 ARG cc_start: 0.8441 (ttt90) cc_final: 0.7951 (ttt90) REVERT: B 377 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6260 (t80) REVERT: B 390 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8685 (mp) REVERT: B 466 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6534 (ptp90) REVERT: B 516 GLU cc_start: 0.7431 (tp30) cc_final: 0.7126 (tp30) REVERT: B 563 GLN cc_start: 0.8072 (mt0) cc_final: 0.7795 (mp10) REVERT: B 571 ASP cc_start: 0.8539 (t0) cc_final: 0.8039 (t0) REVERT: B 586 ASP cc_start: 0.8168 (m-30) cc_final: 0.7787 (m-30) REVERT: B 646 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8479 (mmm160) REVERT: B 762 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7776 (mm110) REVERT: B 773 GLU cc_start: 0.7843 (tt0) cc_final: 0.7627 (tt0) REVERT: B 790 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8684 (mtmm) REVERT: B 811 LYS cc_start: 0.8395 (ttmm) cc_final: 0.7961 (ttmm) REVERT: B 814 LYS cc_start: 0.8861 (mptt) cc_final: 0.8501 (mmtt) REVERT: B 820 ASP cc_start: 0.8592 (t0) cc_final: 0.8251 (m-30) REVERT: B 995 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7880 (mtt-85) REVERT: B 1144 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8372 (mm-30) outliers start: 79 outliers final: 62 residues processed: 527 average time/residue: 0.4193 time to fit residues: 344.1070 Evaluate side-chains 545 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 471 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 235 optimal weight: 0.5980 chunk 264 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 613 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.107631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.085583 restraints weight = 62291.358| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.51 r_work: 0.3176 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 28623 Z= 0.169 Angle : 0.811 15.973 39132 Z= 0.379 Chirality : 0.049 0.455 4695 Planarity : 0.004 0.047 4842 Dihedral : 9.611 104.284 5886 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.56 % Allowed : 17.69 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3333 helix: 1.62 (0.20), residues: 759 sheet: 0.42 (0.19), residues: 651 loop : -1.14 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.005 0.001 HIS A 519 PHE 0.035 0.001 PHE C 133 TYR 0.029 0.002 TYR C 380 ARG 0.011 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 54) link_NAG-ASN : angle 3.21081 ( 162) link_ALPHA1-4 : bond 0.01790 ( 21) link_ALPHA1-4 : angle 3.14638 ( 63) link_BETA1-4 : bond 0.00258 ( 33) link_BETA1-4 : angle 1.45101 ( 99) hydrogen bonds : bond 0.03792 ( 1099) hydrogen bonds : angle 5.54421 ( 3000) link_BETA1-6 : bond 0.01800 ( 3) link_BETA1-6 : angle 2.66149 ( 9) SS BOND : bond 0.00649 ( 45) SS BOND : angle 2.69146 ( 90) covalent geometry : bond 0.00394 (28467) covalent geometry : angle 0.76273 (38709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15426.69 seconds wall clock time: 267 minutes 44.95 seconds (16064.95 seconds total)