Starting phenix.real_space_refine on Tue Apr 7 12:48:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnw_26021/04_2026/7tnw_26021_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnw_26021/04_2026/7tnw_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tnw_26021/04_2026/7tnw_26021_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnw_26021/04_2026/7tnw_26021_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tnw_26021/04_2026/7tnw_26021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnw_26021/04_2026/7tnw_26021.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.038 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/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: 6.99, per 1000 atoms: 0.25 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: 2.83 Conformation dependent library (CDL) restraints added in 1.3 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: 1.47 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: 6.88 Time building geometry restraints manager: 3.69 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: 0.06 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: 10.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.550 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.490 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (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 ARG 0.006 0.001 ARG C1107 TYR 0.110 0.018 TYR A 636 PHE 0.089 0.014 PHE A 133 TRP 0.101 0.023 TRP B 64 HIS 0.011 0.003 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.01394 (28467) covalent geometry : angle 1.81788 (38709) SS BOND : bond 0.00996 ( 45) SS BOND : angle 2.17396 ( 90) hydrogen bonds : bond 0.16875 ( 1099) hydrogen bonds : angle 8.22778 ( 3000) 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) link_BETA1-6 : bond 0.03072 ( 3) link_BETA1-6 : angle 2.65838 ( 9) link_NAG-ASN : bond 0.01620 ( 54) link_NAG-ASN : angle 13.62453 ( 162) *********************** 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 : 1.030 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: 0.7298 (t0) REVERT: C 102 ARG cc_start: 0.7538 (mtt-85) cc_final: 0.6968 (mtt-85) REVERT: C 116 SER cc_start: 0.8734 (p) cc_final: 0.8413 (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: 0.7210 (tt) REVERT: C 191 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7825 (mt-10) REVERT: C 287 ASP cc_start: 0.8527 (t0) cc_final: 0.8059 (t0) REVERT: C 306 PHE cc_start: 0.8873 (m-80) cc_final: 0.8365 (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: 0.6928 (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: 0.7318 (p) REVERT: C 586 ASP cc_start: 0.8209 (m-30) cc_final: 0.7837 (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: 0.8517 (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: 0.8689 (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: 0.8259 (tt) REVERT: C 984 LEU cc_start: 0.8264 (mt) cc_final: 0.8055 (mp) REVERT: C 1125 ASN cc_start: 0.8525 (p0) cc_final: 0.8148 (p0) REVERT: A 99 ASN cc_start: 0.7953 (t0) cc_final: 0.7749 (t0) REVERT: A 116 SER cc_start: 0.8672 (p) cc_final: 0.8447 (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: 0.7541 (mtm-85) REVERT: A 191 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7765 (mt-10) REVERT: A 287 ASP cc_start: 0.8497 (t0) cc_final: 0.8240 (t0) REVERT: A 314 GLN cc_start: 0.8287 (mm110) cc_final: 0.7879 (mm-40) REVERT: A 317 ASN cc_start: 0.8349 (m110) cc_final: 0.7119 (m110) REVERT: A 353 TRP cc_start: 0.8382 (p-90) cc_final: 0.8150 (p-90) REVERT: A 581 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 586 ASP cc_start: 0.8315 (m-30) cc_final: 0.7969 (m-30) REVERT: A 615 VAL cc_start: 0.8660 (t) cc_final: 0.8207 (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: 0.7278 (pp30) REVERT: A 737 ASP cc_start: 0.7853 (t0) cc_final: 0.7528 (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: 0.8366 (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: 0.7864 (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: 0.8289 (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: 0.7303 (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: 0.7419 (t0) REVERT: B 765 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.8158 (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: 0.8036 (t0) REVERT: B 837 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.6117 (t80) outliers start: 53 outliers final: 10 residues processed: 707 average time/residue: 0.2107 time to fit residues: 228.9042 Evaluate side-chains 530 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 513 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 GLN A 121 ASN A 394 ASN A 417 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 836 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN B 481 ASN B 613 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.109212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086813 restraints weight = 61988.414| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.55 r_work: 0.3190 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28623 Z= 0.185 Angle : 0.913 18.976 39132 Z= 0.431 Chirality : 0.056 0.756 4695 Planarity : 0.004 0.044 4842 Dihedral : 14.211 112.609 5920 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.83 % Allowed : 9.78 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3333 helix: 0.72 (0.19), residues: 750 sheet: 0.19 (0.18), residues: 699 loop : -1.26 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 493 TYR 0.020 0.002 TYR C 265 PHE 0.027 0.002 PHE A1148 TRP 0.021 0.002 TRP C 64 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00417 (28467) covalent geometry : angle 0.82298 (38709) SS BOND : bond 0.00316 ( 45) SS BOND : angle 2.96218 ( 90) hydrogen bonds : bond 0.05089 ( 1099) hydrogen bonds : angle 6.20153 ( 3000) link_ALPHA1-4 : bond 0.01512 ( 21) link_ALPHA1-4 : angle 2.42461 ( 63) link_BETA1-4 : bond 0.00340 ( 33) link_BETA1-4 : angle 2.02153 ( 99) link_BETA1-6 : bond 0.01496 ( 3) link_BETA1-6 : angle 1.73616 ( 9) link_NAG-ASN : bond 0.00685 ( 54) link_NAG-ASN : angle 5.46909 ( 162) *********************** 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 626 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 543 time to evaluate : 1.037 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: 0.8729 (mmmm) cc_final: 0.8398 (mmmm) REVERT: C 99 ASN cc_start: 0.8283 (t0) cc_final: 0.7783 (t0) REVERT: C 102 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7529 (mtt-85) REVERT: C 121 ASN cc_start: 0.6609 (t0) cc_final: 0.6330 (t0) REVERT: C 140 PHE cc_start: 0.7994 (p90) cc_final: 0.7787 (p90) REVERT: C 191 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7954 (mt-10) REVERT: C 239 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7592 (tm-30) REVERT: C 271 GLN cc_start: 0.8863 (mt0) cc_final: 0.8663 (mt0) REVERT: C 287 ASP cc_start: 0.8472 (t0) cc_final: 0.8145 (t0) REVERT: C 306 PHE cc_start: 0.9003 (m-80) cc_final: 0.8636 (m-80) REVERT: C 317 ASN cc_start: 0.8404 (m110) cc_final: 0.7716 (m110) REVERT: C 586 ASP cc_start: 0.8203 (m-30) cc_final: 0.7789 (m-30) REVERT: C 654 GLU cc_start: 0.8302 (tt0) cc_final: 0.7946 (tt0) REVERT: C 675 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7271 (pp30) REVERT: C 690 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7572 (mm-40) REVERT: C 693 ILE cc_start: 0.9406 (pt) cc_final: 0.9071 (pt) REVERT: C 790 LYS cc_start: 0.9021 (mtmt) cc_final: 0.8777 (mtpp) REVERT: C 811 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8130 (ttmm) REVERT: C 950 ASP cc_start: 0.8300 (m-30) cc_final: 0.8070 (m-30) REVERT: C 1125 ASN cc_start: 0.8555 (p0) cc_final: 0.6743 (p0) REVERT: A 41 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8541 (mmmm) REVERT: A 51 THR cc_start: 0.8877 (t) cc_final: 0.8671 (p) REVERT: A 137 ASN cc_start: 0.8693 (t0) cc_final: 0.8403 (p0) REVERT: A 191 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7802 (mt-10) REVERT: A 239 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 287 ASP cc_start: 0.8529 (t0) cc_final: 0.8283 (t0) REVERT: A 581 THR cc_start: 0.8724 (p) cc_final: 0.8387 (p) REVERT: A 586 ASP cc_start: 0.8317 (m-30) cc_final: 0.7993 (m-30) REVERT: A 632 THR cc_start: 0.8411 (m) cc_final: 0.8055 (p) REVERT: A 654 GLU cc_start: 0.8270 (tt0) cc_final: 0.7902 (tt0) REVERT: A 675 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7277 (pp30) REVERT: A 693 ILE cc_start: 0.9370 (pt) cc_final: 0.9147 (pt) REVERT: A 737 ASP cc_start: 0.7899 (t0) cc_final: 0.7611 (t0) REVERT: A 755 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8577 (mm-40) REVERT: A 773 GLU cc_start: 0.8315 (tp30) cc_final: 0.8113 (tt0) REVERT: A 776 LYS cc_start: 0.9048 (tttp) cc_final: 0.8748 (tttp) REVERT: A 780 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8152 (mt-10) REVERT: A 790 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8711 (mtpp) REVERT: A 820 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8248 (m-30) REVERT: A 950 ASP cc_start: 0.8227 (m-30) cc_final: 0.7835 (m-30) REVERT: A 984 LEU cc_start: 0.7683 (mp) cc_final: 0.7456 (mt) REVERT: A 988 GLU cc_start: 0.7565 (pp20) cc_final: 0.7097 (pp20) REVERT: A 1005 GLN cc_start: 0.8593 (tp40) cc_final: 0.8138 (tp40) REVERT: A 1125 ASN cc_start: 0.8604 (p0) cc_final: 0.7919 (p0) REVERT: B 41 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8419 (mmmm) REVERT: B 99 ASN cc_start: 0.8104 (t0) cc_final: 0.7884 (t0) REVERT: B 105 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8511 (mp) REVERT: B 121 ASN cc_start: 0.6450 (t0) cc_final: 0.6203 (t0) REVERT: B 153 MET cc_start: 0.6085 (tmm) cc_final: 0.5689 (tmm) REVERT: B 191 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7795 (mt-10) REVERT: B 239 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 317 ASN cc_start: 0.8181 (m110) cc_final: 0.7936 (m110) REVERT: B 323 THR cc_start: 0.8581 (p) cc_final: 0.8299 (p) REVERT: B 338 PHE cc_start: 0.7254 (m-80) cc_final: 0.6856 (m-80) REVERT: B 355 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7765 (ttt90) REVERT: B 369 TYR cc_start: 0.7109 (t80) cc_final: 0.6802 (t80) REVERT: B 466 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6161 (ptp90) REVERT: B 557 LYS cc_start: 0.9064 (mtmm) cc_final: 0.8840 (mtmt) REVERT: B 581 THR cc_start: 0.8549 (p) cc_final: 0.8278 (p) REVERT: B 615 VAL cc_start: 0.8821 (t) cc_final: 0.8607 (p) REVERT: B 646 ARG cc_start: 0.8926 (tpp80) cc_final: 0.8685 (mmm160) REVERT: B 649 CYS cc_start: 0.7542 (t) cc_final: 0.7144 (t) REVERT: B 737 ASP cc_start: 0.7673 (t0) cc_final: 0.7446 (t0) REVERT: B 762 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7880 (mm-40) REVERT: B 790 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8654 (mtpp) REVERT: B 957 GLN cc_start: 0.8508 (tt0) cc_final: 0.8236 (tm-30) REVERT: B 964 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8758 (mtmm) REVERT: B 995 ARG cc_start: 0.8249 (mtt-85) cc_final: 0.7868 (mtt-85) outliers start: 83 outliers final: 39 residues processed: 589 average time/residue: 0.2008 time to fit residues: 183.7267 Evaluate side-chains 510 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 465 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 486 PHE Chi-restraints excluded: chain C residue 551 VAL 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 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 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 154 optimal weight: 0.3980 chunk 89 optimal weight: 0.4980 chunk 273 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 chunk 287 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 59 optimal weight: 0.3980 chunk 222 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 218 GLN A 417 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 519 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.109073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086646 restraints weight = 62266.043| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.55 r_work: 0.3190 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2675 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 : 0.812 15.289 39132 Z= 0.380 Chirality : 0.051 0.602 4695 Planarity : 0.004 0.045 4842 Dihedral : 13.193 109.140 5897 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.90 % Allowed : 12.00 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3333 helix: 1.10 (0.19), residues: 771 sheet: 0.24 (0.19), residues: 711 loop : -1.19 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 190 TYR 0.020 0.001 TYR C1067 PHE 0.022 0.002 PHE A 168 TRP 0.026 0.002 TRP B 436 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00360 (28467) covalent geometry : angle 0.74446 (38709) SS BOND : bond 0.00508 ( 45) SS BOND : angle 2.03451 ( 90) hydrogen bonds : bond 0.04400 ( 1099) hydrogen bonds : angle 5.82913 ( 3000) link_ALPHA1-4 : bond 0.01564 ( 21) link_ALPHA1-4 : angle 2.53409 ( 63) link_BETA1-4 : bond 0.00304 ( 33) link_BETA1-4 : angle 1.67922 ( 99) link_BETA1-6 : bond 0.01502 ( 3) link_BETA1-6 : angle 1.91197 ( 9) link_NAG-ASN : bond 0.00603 ( 54) link_NAG-ASN : angle 4.48292 ( 162) *********************** 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 603 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 518 time to evaluate : 1.007 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: 0.8736 (mmmm) cc_final: 0.8280 (mmmm) REVERT: C 99 ASN cc_start: 0.8326 (t0) cc_final: 0.8013 (t0) REVERT: C 102 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7614 (mmt90) REVERT: C 121 ASN cc_start: 0.6396 (t0) cc_final: 0.6091 (t0) REVERT: C 191 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8062 (mt-10) REVERT: C 239 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7613 (tm-30) REVERT: C 271 GLN cc_start: 0.8911 (mt0) cc_final: 0.8671 (mt0) REVERT: C 287 ASP cc_start: 0.8480 (t0) cc_final: 0.8116 (t0) REVERT: C 306 PHE cc_start: 0.9028 (m-80) cc_final: 0.8650 (m-80) REVERT: C 317 ASN cc_start: 0.8372 (m110) cc_final: 0.7661 (m110) REVERT: C 398 ASP cc_start: 0.7160 (m-30) cc_final: 0.6650 (t0) REVERT: C 586 ASP cc_start: 0.8217 (m-30) cc_final: 0.7794 (m-30) REVERT: C 654 GLU cc_start: 0.8334 (tt0) cc_final: 0.7963 (tt0) REVERT: C 675 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7266 (pp30) REVERT: C 690 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7660 (mm-40) REVERT: C 693 ILE cc_start: 0.9386 (pt) cc_final: 0.9081 (pt) REVERT: C 790 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8720 (mtpp) REVERT: C 811 LYS cc_start: 0.8449 (ttmm) cc_final: 0.7867 (ttmm) REVERT: C 820 ASP cc_start: 0.8546 (t0) cc_final: 0.8187 (m-30) REVERT: C 823 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: C 1072 GLU cc_start: 0.8817 (pm20) cc_final: 0.8553 (pm20) REVERT: C 1125 ASN cc_start: 0.8809 (p0) cc_final: 0.8300 (p0) REVERT: C 1127 ASP cc_start: 0.8600 (p0) cc_final: 0.8292 (p0) REVERT: A 41 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8411 (mmmm) REVERT: A 116 SER cc_start: 0.8742 (m) cc_final: 0.8460 (p) REVERT: A 190 ARG cc_start: 0.8432 (mtt90) cc_final: 0.8014 (mtt90) REVERT: A 191 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 287 ASP cc_start: 0.8544 (t0) cc_final: 0.8274 (t0) REVERT: A 390 LEU cc_start: 0.8886 (mp) cc_final: 0.8685 (mp) REVERT: A 581 THR cc_start: 0.8727 (p) cc_final: 0.8385 (p) REVERT: A 586 ASP cc_start: 0.8360 (m-30) cc_final: 0.8107 (m-30) REVERT: A 632 THR cc_start: 0.8406 (m) cc_final: 0.7989 (p) REVERT: A 654 GLU cc_start: 0.8294 (tt0) cc_final: 0.7907 (tt0) REVERT: A 675 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7261 (pp30) REVERT: A 693 ILE cc_start: 0.9361 (pt) cc_final: 0.9082 (pt) REVERT: A 737 ASP cc_start: 0.7949 (t0) cc_final: 0.7640 (t0) REVERT: A 755 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8611 (mm-40) REVERT: A 773 GLU cc_start: 0.8330 (tp30) cc_final: 0.8083 (tt0) REVERT: A 776 LYS cc_start: 0.8938 (tttp) cc_final: 0.8704 (tttp) REVERT: A 790 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8719 (mtpp) REVERT: A 820 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: A 950 ASP cc_start: 0.8196 (m-30) cc_final: 0.7962 (m-30) REVERT: A 988 GLU cc_start: 0.7614 (pp20) cc_final: 0.7034 (pp20) REVERT: A 1005 GLN cc_start: 0.8635 (tp40) cc_final: 0.8279 (tp40) REVERT: A 1072 GLU cc_start: 0.8717 (pm20) cc_final: 0.8284 (pm20) REVERT: A 1125 ASN cc_start: 0.8655 (p0) cc_final: 0.7524 (p0) REVERT: A 1127 ASP cc_start: 0.8381 (p0) cc_final: 0.7974 (p0) REVERT: B 41 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8343 (mmmm) REVERT: B 99 ASN cc_start: 0.8114 (t0) cc_final: 0.7892 (t0) REVERT: B 129 LYS cc_start: 0.8026 (tttt) cc_final: 0.7689 (ptmm) REVERT: B 153 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.5413 (tmm) REVERT: B 186 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6076 (m-80) REVERT: B 191 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 239 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7761 (tm-30) REVERT: B 317 ASN cc_start: 0.8214 (m110) cc_final: 0.7934 (m110) REVERT: B 323 THR cc_start: 0.8750 (p) cc_final: 0.8538 (p) REVERT: B 355 ARG cc_start: 0.8374 (ttt90) cc_final: 0.7830 (ttt90) REVERT: B 369 TYR cc_start: 0.7352 (t80) cc_final: 0.7119 (t80) REVERT: B 422 ASN cc_start: 0.6163 (p0) cc_final: 0.4576 (p0) REVERT: B 455 LEU cc_start: 0.8320 (tp) cc_final: 0.8003 (mt) REVERT: B 557 LYS cc_start: 0.9112 (mtmm) cc_final: 0.8873 (mtmt) REVERT: B 581 THR cc_start: 0.8552 (p) cc_final: 0.8285 (p) REVERT: B 646 ARG cc_start: 0.8983 (tpp80) cc_final: 0.8695 (mmm160) REVERT: B 762 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7816 (mm-40) REVERT: B 790 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8624 (mtpp) REVERT: B 811 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8114 (ttmm) REVERT: B 820 ASP cc_start: 0.8602 (t0) cc_final: 0.8263 (m-30) REVERT: B 957 GLN cc_start: 0.8516 (tt0) cc_final: 0.8288 (tm-30) REVERT: B 964 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8797 (mtmm) REVERT: B 995 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.7852 (mtt-85) outliers start: 85 outliers final: 46 residues processed: 560 average time/residue: 0.2002 time to fit residues: 175.0814 Evaluate side-chains 525 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 472 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 223 LEU 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 551 VAL 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 823 PHE 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 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 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 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 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 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 159 optimal weight: 2.9990 chunk 80 optimal weight: 0.0570 chunk 185 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 292 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN A 121 ASN A 314 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.108142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085803 restraints weight = 61625.485| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.51 r_work: 0.3176 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 28623 Z= 0.181 Angle : 0.808 14.380 39132 Z= 0.378 Chirality : 0.050 0.545 4695 Planarity : 0.004 0.044 4842 Dihedral : 12.677 107.424 5893 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.24 % Allowed : 13.16 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3333 helix: 1.33 (0.20), residues: 762 sheet: 0.30 (0.19), residues: 669 loop : -1.20 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 190 TYR 0.020 0.002 TYR C1067 PHE 0.035 0.002 PHE C 338 TRP 0.033 0.002 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00418 (28467) covalent geometry : angle 0.74431 (38709) SS BOND : bond 0.00488 ( 45) SS BOND : angle 2.72979 ( 90) hydrogen bonds : bond 0.04196 ( 1099) hydrogen bonds : angle 5.77864 ( 3000) link_ALPHA1-4 : bond 0.01643 ( 21) link_ALPHA1-4 : angle 2.65320 ( 63) link_BETA1-4 : bond 0.00249 ( 33) link_BETA1-4 : angle 1.63732 ( 99) link_BETA1-6 : bond 0.01432 ( 3) link_BETA1-6 : angle 2.16367 ( 9) link_NAG-ASN : bond 0.00573 ( 54) link_NAG-ASN : angle 4.07171 ( 162) *********************** 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 592 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 497 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 LYS cc_start: 0.8749 (mmmm) cc_final: 0.8340 (mmmm) REVERT: C 99 ASN cc_start: 0.8421 (t0) cc_final: 0.8167 (t0) REVERT: C 102 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7673 (mmt90) REVERT: C 121 ASN cc_start: 0.6416 (t0) cc_final: 0.6114 (t0) REVERT: C 129 LYS cc_start: 0.8006 (tttt) cc_final: 0.7735 (ptmm) REVERT: C 191 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7963 (mt-10) REVERT: C 271 GLN cc_start: 0.8884 (mt0) cc_final: 0.8624 (mt0) REVERT: C 287 ASP cc_start: 0.8508 (t0) cc_final: 0.8129 (t0) REVERT: C 306 PHE cc_start: 0.9047 (m-80) cc_final: 0.8636 (m-80) REVERT: C 317 ASN cc_start: 0.8338 (m110) cc_final: 0.7583 (m110) REVERT: C 377 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6398 (t80) REVERT: C 398 ASP cc_start: 0.7239 (m-30) cc_final: 0.6693 (t0) REVERT: C 558 LYS cc_start: 0.8988 (mptt) cc_final: 0.8785 (mmmm) REVERT: C 586 ASP cc_start: 0.8229 (m-30) cc_final: 0.7797 (m-30) REVERT: C 654 GLU cc_start: 0.8378 (tt0) cc_final: 0.7966 (tt0) REVERT: C 675 GLN cc_start: 0.7738 (pt0) cc_final: 0.7270 (pp30) REVERT: C 690 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7719 (mm-40) REVERT: C 693 ILE cc_start: 0.9379 (pt) cc_final: 0.9079 (pt) REVERT: C 762 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7833 (mm110) REVERT: C 776 LYS cc_start: 0.8917 (tttm) cc_final: 0.8568 (tttm) REVERT: C 790 LYS cc_start: 0.8988 (mtmt) cc_final: 0.8687 (mtpp) REVERT: C 811 LYS cc_start: 0.8459 (ttmm) cc_final: 0.7910 (ttmm) REVERT: C 820 ASP cc_start: 0.8521 (t0) cc_final: 0.8140 (m-30) REVERT: C 977 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8078 (mp) REVERT: C 1072 GLU cc_start: 0.8864 (pm20) cc_final: 0.8594 (pm20) REVERT: C 1125 ASN cc_start: 0.8782 (p0) cc_final: 0.7837 (p0) REVERT: C 1127 ASP cc_start: 0.8578 (p0) cc_final: 0.8127 (p0) REVERT: A 41 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8369 (mmmm) REVERT: A 116 SER cc_start: 0.8718 (m) cc_final: 0.8411 (p) REVERT: A 129 LYS cc_start: 0.8055 (tttt) cc_final: 0.7674 (ptmm) REVERT: A 190 ARG cc_start: 0.8397 (mtt90) cc_final: 0.7918 (mtt90) REVERT: A 191 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7837 (mt-10) REVERT: A 287 ASP cc_start: 0.8538 (t0) cc_final: 0.8302 (t0) REVERT: A 377 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6520 (t80) REVERT: A 571 ASP cc_start: 0.8575 (t0) cc_final: 0.8297 (t0) REVERT: A 581 THR cc_start: 0.8716 (p) cc_final: 0.8387 (p) REVERT: A 586 ASP cc_start: 0.8356 (m-30) cc_final: 0.7923 (m-30) REVERT: A 632 THR cc_start: 0.8385 (m) cc_final: 0.7930 (p) REVERT: A 654 GLU cc_start: 0.8387 (tt0) cc_final: 0.7973 (tt0) REVERT: A 737 ASP cc_start: 0.8034 (t0) cc_final: 0.7649 (t0) REVERT: A 755 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8608 (mm-40) REVERT: A 773 GLU cc_start: 0.8301 (tp30) cc_final: 0.8027 (tt0) REVERT: A 776 LYS cc_start: 0.8924 (tttp) cc_final: 0.8661 (tttp) REVERT: A 790 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8738 (mtpp) REVERT: A 814 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8661 (mmtm) REVERT: A 820 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: A 950 ASP cc_start: 0.8243 (m-30) cc_final: 0.7878 (m-30) REVERT: A 977 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8343 (mp) REVERT: A 988 GLU cc_start: 0.7699 (pp20) cc_final: 0.7121 (pp20) REVERT: A 1005 GLN cc_start: 0.8643 (tp40) cc_final: 0.8322 (tp40) REVERT: A 1072 GLU cc_start: 0.8735 (pm20) cc_final: 0.8288 (pm20) REVERT: A 1125 ASN cc_start: 0.8663 (p0) cc_final: 0.8161 (p0) REVERT: A 1127 ASP cc_start: 0.8368 (p0) cc_final: 0.8109 (p0) REVERT: B 41 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8325 (mmmm) REVERT: B 95 ILE cc_start: 0.9089 (mm) cc_final: 0.8812 (tp) REVERT: B 99 ASN cc_start: 0.8275 (t0) cc_final: 0.8058 (t0) REVERT: B 129 LYS cc_start: 0.8077 (tttt) cc_final: 0.7833 (ptmm) REVERT: B 153 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.5331 (tmm) REVERT: B 186 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6131 (m-80) REVERT: B 191 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7930 (mt-10) REVERT: B 317 ASN cc_start: 0.8221 (m110) cc_final: 0.7976 (m110) REVERT: B 355 ARG cc_start: 0.8426 (ttt90) cc_final: 0.7925 (ttt90) REVERT: B 377 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.6293 (t80) REVERT: B 400 PHE cc_start: 0.7463 (p90) cc_final: 0.7117 (p90) REVERT: B 466 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6533 (ptp90) REVERT: B 516 GLU cc_start: 0.7330 (tp30) cc_final: 0.7115 (tp30) REVERT: B 557 LYS cc_start: 0.9100 (mtmm) cc_final: 0.8871 (mtmt) REVERT: B 581 THR cc_start: 0.8637 (p) cc_final: 0.8391 (p) REVERT: B 646 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8698 (mmm160) REVERT: B 762 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7800 (mm-40) REVERT: B 790 LYS cc_start: 0.8944 (mtmt) cc_final: 0.8608 (mtpp) REVERT: B 804 GLN cc_start: 0.8799 (mt0) cc_final: 0.7816 (mt0) REVERT: B 811 LYS cc_start: 0.8466 (ttmm) cc_final: 0.8210 (ttmm) REVERT: B 820 ASP cc_start: 0.8569 (t0) cc_final: 0.8210 (m-30) REVERT: B 935 GLN cc_start: 0.7903 (mt0) cc_final: 0.7276 (mt0) REVERT: B 957 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: B 995 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.7937 (mtt-85) outliers start: 95 outliers final: 53 residues processed: 549 average time/residue: 0.1984 time to fit residues: 169.5843 Evaluate side-chains 534 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 471 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 307 THR Chi-restraints excluded: chain C residue 377 PHE 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 933 LYS 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 984 LEU 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 120 VAL 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 377 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 455 LEU 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 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 984 LEU Chi-restraints excluded: chain A residue 991 VAL 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 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 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 957 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 3 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 318 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 191 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 354 ASN A 613 GLN A1011 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.107256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085318 restraints weight = 61530.870| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.46 r_work: 0.3170 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 28623 Z= 0.183 Angle : 0.797 14.392 39132 Z= 0.371 Chirality : 0.050 0.513 4695 Planarity : 0.004 0.044 4842 Dihedral : 12.066 106.665 5886 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.24 % Allowed : 13.77 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3333 helix: 1.24 (0.20), residues: 774 sheet: 0.47 (0.20), residues: 624 loop : -1.11 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 237 TYR 0.020 0.002 TYR C1067 PHE 0.036 0.002 PHE B 338 TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00419 (28467) covalent geometry : angle 0.73881 (38709) SS BOND : bond 0.00484 ( 45) SS BOND : angle 2.62194 ( 90) hydrogen bonds : bond 0.04063 ( 1099) hydrogen bonds : angle 5.70098 ( 3000) link_ALPHA1-4 : bond 0.01693 ( 21) link_ALPHA1-4 : angle 2.90008 ( 63) link_BETA1-4 : bond 0.00249 ( 33) link_BETA1-4 : angle 1.56800 ( 99) link_BETA1-6 : bond 0.01394 ( 3) link_BETA1-6 : angle 2.31118 ( 9) link_NAG-ASN : bond 0.00555 ( 54) link_NAG-ASN : angle 3.74952 ( 162) *********************** 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 598 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 503 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 LYS cc_start: 0.8747 (mmmm) cc_final: 0.8406 (mmtp) REVERT: C 99 ASN cc_start: 0.8373 (t0) cc_final: 0.8164 (t0) REVERT: C 102 ARG cc_start: 0.8048 (mtt-85) cc_final: 0.7637 (mmt90) REVERT: C 121 ASN cc_start: 0.6469 (t0) cc_final: 0.6224 (t0) REVERT: C 129 LYS cc_start: 0.8015 (tttt) cc_final: 0.7781 (ptmm) REVERT: C 187 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8151 (tptt) REVERT: C 191 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7961 (mt-10) REVERT: C 239 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7766 (tm-30) REVERT: C 271 GLN cc_start: 0.8898 (mt0) cc_final: 0.8625 (mt0) REVERT: C 287 ASP cc_start: 0.8517 (t0) cc_final: 0.8299 (t0) REVERT: C 317 ASN cc_start: 0.8323 (m110) cc_final: 0.7695 (m110) REVERT: C 377 PHE cc_start: 0.6784 (OUTLIER) cc_final: 0.6450 (t80) REVERT: C 390 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8816 (mp) REVERT: C 398 ASP cc_start: 0.7142 (m-30) cc_final: 0.6598 (t0) REVERT: C 558 LYS cc_start: 0.9037 (mptt) cc_final: 0.8813 (mmmm) REVERT: C 563 GLN cc_start: 0.8022 (mt0) cc_final: 0.7656 (mp10) REVERT: C 586 ASP cc_start: 0.8214 (m-30) cc_final: 0.7784 (m-30) REVERT: C 649 CYS cc_start: 0.7162 (t) cc_final: 0.6725 (t) REVERT: C 654 GLU cc_start: 0.8344 (tt0) cc_final: 0.7911 (tt0) REVERT: C 693 ILE cc_start: 0.9391 (pt) cc_final: 0.9115 (pt) REVERT: C 762 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7741 (mm110) REVERT: C 776 LYS cc_start: 0.8900 (tttm) cc_final: 0.8605 (tttm) REVERT: C 790 LYS cc_start: 0.8956 (mtmt) cc_final: 0.8646 (mtpp) REVERT: C 811 LYS cc_start: 0.8467 (ttmm) cc_final: 0.7879 (ttmm) REVERT: C 820 ASP cc_start: 0.8516 (t0) cc_final: 0.8134 (m-30) REVERT: C 977 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8130 (mp) REVERT: C 1072 GLU cc_start: 0.8870 (pm20) cc_final: 0.8611 (pm20) REVERT: A 41 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8436 (mmmm) REVERT: A 116 SER cc_start: 0.8697 (m) cc_final: 0.8407 (p) REVERT: A 129 LYS cc_start: 0.8067 (tttt) cc_final: 0.7695 (ptmm) REVERT: A 135 PHE cc_start: 0.7605 (m-80) cc_final: 0.7258 (m-80) REVERT: A 191 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 287 ASP cc_start: 0.8504 (t0) cc_final: 0.8276 (t0) REVERT: A 377 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6617 (t80) REVERT: A 571 ASP cc_start: 0.8556 (t0) cc_final: 0.8330 (t0) REVERT: A 581 THR cc_start: 0.8718 (p) cc_final: 0.8447 (p) REVERT: A 586 ASP cc_start: 0.8337 (m-30) cc_final: 0.7967 (m-30) REVERT: A 654 GLU cc_start: 0.8408 (tt0) cc_final: 0.7993 (tt0) REVERT: A 675 GLN cc_start: 0.7394 (pp30) cc_final: 0.7089 (pp30) REVERT: A 690 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7617 (mm110) REVERT: A 737 ASP cc_start: 0.8105 (t0) cc_final: 0.7780 (t0) REVERT: A 755 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8504 (mp10) REVERT: A 773 GLU cc_start: 0.8243 (tp30) cc_final: 0.8025 (tt0) REVERT: A 776 LYS cc_start: 0.8916 (tttp) cc_final: 0.8642 (tttp) REVERT: A 790 LYS cc_start: 0.9003 (mtmt) cc_final: 0.8755 (mtpp) REVERT: A 820 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: A 950 ASP cc_start: 0.8264 (m-30) cc_final: 0.7860 (m-30) REVERT: A 977 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8359 (mp) REVERT: A 988 GLU cc_start: 0.7680 (pp20) cc_final: 0.7090 (pp20) REVERT: A 1005 GLN cc_start: 0.8650 (tp40) cc_final: 0.8348 (tp40) REVERT: A 1072 GLU cc_start: 0.8718 (pm20) cc_final: 0.8254 (pm20) REVERT: A 1125 ASN cc_start: 0.8692 (p0) cc_final: 0.8285 (p0) REVERT: A 1127 ASP cc_start: 0.8385 (p0) cc_final: 0.8157 (p0) REVERT: B 80 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6693 (p0) REVERT: B 95 ILE cc_start: 0.9072 (mm) cc_final: 0.8320 (tp) REVERT: B 99 ASN cc_start: 0.8293 (t0) cc_final: 0.7140 (t0) REVERT: B 102 ARG cc_start: 0.7814 (mtt-85) cc_final: 0.7050 (mmt90) REVERT: B 129 LYS cc_start: 0.8091 (tttt) cc_final: 0.7860 (ptmm) REVERT: B 153 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5380 (tmm) REVERT: B 187 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8293 (tttp) REVERT: B 190 ARG cc_start: 0.8573 (mtt90) cc_final: 0.8195 (mtt90) REVERT: B 191 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7948 (mt-10) REVERT: B 317 ASN cc_start: 0.8261 (m110) cc_final: 0.8029 (m110) REVERT: B 355 ARG cc_start: 0.8410 (ttt90) cc_final: 0.7917 (ttt90) REVERT: B 377 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.6374 (t80) REVERT: B 390 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8734 (mp) REVERT: B 400 PHE cc_start: 0.7471 (p90) cc_final: 0.7065 (p90) REVERT: B 455 LEU cc_start: 0.8421 (tp) cc_final: 0.8088 (mt) REVERT: B 466 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6488 (ptp90) REVERT: B 516 GLU cc_start: 0.7416 (tp30) cc_final: 0.7179 (tp30) REVERT: B 557 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8848 (mtmt) REVERT: B 581 THR cc_start: 0.8655 (p) cc_final: 0.8364 (p) REVERT: B 646 ARG cc_start: 0.9031 (tpp80) cc_final: 0.8705 (mmm160) REVERT: B 762 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7700 (mm110) REVERT: B 773 GLU cc_start: 0.7792 (tt0) cc_final: 0.7584 (tt0) REVERT: B 790 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8589 (mtpp) REVERT: B 811 LYS cc_start: 0.8431 (ttmm) cc_final: 0.8094 (ttmm) REVERT: B 820 ASP cc_start: 0.8545 (t0) cc_final: 0.8178 (m-30) REVERT: B 957 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: B 995 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7909 (mtt-85) REVERT: B 1019 ARG cc_start: 0.8555 (ttt90) cc_final: 0.8294 (tpt90) outliers start: 95 outliers final: 63 residues processed: 555 average time/residue: 0.2033 time to fit residues: 175.1220 Evaluate side-chains 554 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 478 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 187 LYS 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 434 ILE 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 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 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 984 LEU 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 120 VAL 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 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 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 984 LEU Chi-restraints excluded: chain A residue 991 VAL 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 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 524 VAL 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 957 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 111 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 324 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 311 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1011 GLN A 121 ASN A 314 GLN A 354 ASN A 417 ASN A 613 GLN B 30 ASN B 121 ASN B 314 GLN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.107298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084627 restraints weight = 61281.953| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.60 r_work: 0.3131 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 28623 Z= 0.259 Angle : 0.836 14.564 39132 Z= 0.392 Chirality : 0.052 0.534 4695 Planarity : 0.004 0.044 4842 Dihedral : 11.909 106.628 5886 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.72 % Allowed : 14.62 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3333 helix: 1.29 (0.20), residues: 765 sheet: 0.34 (0.19), residues: 621 loop : -1.21 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 237 TYR 0.021 0.002 TYR C1067 PHE 0.016 0.002 PHE B 86 TRP 0.009 0.001 TRP A 353 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00600 (28467) covalent geometry : angle 0.77744 (38709) SS BOND : bond 0.00601 ( 45) SS BOND : angle 2.71939 ( 90) hydrogen bonds : bond 0.04339 ( 1099) hydrogen bonds : angle 5.68525 ( 3000) link_ALPHA1-4 : bond 0.01742 ( 21) link_ALPHA1-4 : angle 3.01076 ( 63) link_BETA1-4 : bond 0.00235 ( 33) link_BETA1-4 : angle 1.61485 ( 99) link_BETA1-6 : bond 0.01356 ( 3) link_BETA1-6 : angle 2.55628 ( 9) link_NAG-ASN : bond 0.00594 ( 54) link_NAG-ASN : angle 3.85937 ( 162) *********************** 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 605 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 496 time to evaluate : 1.091 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: 0.8749 (mmmm) cc_final: 0.8366 (mmmm) REVERT: C 102 ARG cc_start: 0.8122 (mtt-85) cc_final: 0.7694 (mmt90) REVERT: C 121 ASN cc_start: 0.6605 (t0) cc_final: 0.6323 (t0) REVERT: C 129 LYS cc_start: 0.8023 (tttt) cc_final: 0.7750 (ptmm) REVERT: C 191 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7979 (mt-10) REVERT: C 271 GLN cc_start: 0.8925 (mt0) cc_final: 0.8667 (mt0) REVERT: C 317 ASN cc_start: 0.8315 (m110) cc_final: 0.7891 (m110) REVERT: C 377 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6566 (t80) REVERT: C 398 ASP cc_start: 0.7115 (m-30) cc_final: 0.6579 (t0) REVERT: C 558 LYS cc_start: 0.9083 (mptt) cc_final: 0.8859 (mmmm) REVERT: C 586 ASP cc_start: 0.8249 (m-30) cc_final: 0.7844 (m-30) REVERT: C 649 CYS cc_start: 0.7142 (t) cc_final: 0.6701 (t) REVERT: C 654 GLU cc_start: 0.8335 (tt0) cc_final: 0.7896 (tt0) REVERT: C 675 GLN cc_start: 0.7643 (pp30) cc_final: 0.7102 (pp30) REVERT: C 690 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7599 (mm-40) REVERT: C 762 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7824 (mm110) REVERT: C 790 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8698 (mtpp) REVERT: C 820 ASP cc_start: 0.8545 (t0) cc_final: 0.8158 (m-30) REVERT: C 977 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8186 (mp) REVERT: C 1072 GLU cc_start: 0.8895 (pm20) cc_final: 0.8633 (pm20) REVERT: C 1148 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.6220 (p90) REVERT: A 41 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8425 (mmmm) REVERT: A 116 SER cc_start: 0.8714 (m) cc_final: 0.8433 (p) REVERT: A 137 ASN cc_start: 0.8626 (m110) cc_final: 0.7913 (p0) REVERT: A 191 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7922 (mt-10) REVERT: A 287 ASP cc_start: 0.8540 (t0) cc_final: 0.8311 (t0) REVERT: A 377 PHE cc_start: 0.6956 (OUTLIER) cc_final: 0.6567 (t80) REVERT: A 581 THR cc_start: 0.8752 (p) cc_final: 0.8496 (p) REVERT: A 586 ASP cc_start: 0.8361 (m-30) cc_final: 0.7959 (m-30) REVERT: A 654 GLU cc_start: 0.8437 (tt0) cc_final: 0.8034 (tt0) REVERT: A 737 ASP cc_start: 0.8141 (t0) cc_final: 0.7847 (t0) REVERT: A 755 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8536 (mp10) REVERT: A 773 GLU cc_start: 0.8287 (tp30) cc_final: 0.8074 (tt0) REVERT: A 776 LYS cc_start: 0.8930 (tttp) cc_final: 0.8622 (tttp) REVERT: A 790 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8752 (mtpp) REVERT: A 820 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8143 (m-30) REVERT: A 950 ASP cc_start: 0.8317 (m-30) cc_final: 0.7964 (m-30) REVERT: A 977 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8438 (mp) REVERT: A 988 GLU cc_start: 0.7822 (pp20) cc_final: 0.7234 (pp20) REVERT: A 1005 GLN cc_start: 0.8704 (tp40) cc_final: 0.8381 (tp40) REVERT: A 1072 GLU cc_start: 0.8776 (pm20) cc_final: 0.8291 (pm20) REVERT: A 1125 ASN cc_start: 0.8728 (p0) cc_final: 0.8369 (p0) REVERT: A 1127 ASP cc_start: 0.8424 (p0) cc_final: 0.8218 (p0) REVERT: B 41 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8334 (mmmm) REVERT: B 95 ILE cc_start: 0.9071 (mm) cc_final: 0.8724 (tp) REVERT: B 129 LYS cc_start: 0.8142 (tttt) cc_final: 0.7832 (ptmm) REVERT: B 153 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5372 (tmm) REVERT: B 186 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6326 (m-80) REVERT: B 191 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7929 (mt-10) REVERT: B 317 ASN cc_start: 0.8274 (m110) cc_final: 0.8048 (m110) REVERT: B 355 ARG cc_start: 0.8477 (ttt90) cc_final: 0.7994 (ttt90) REVERT: B 377 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6178 (t80) REVERT: B 390 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8818 (mp) REVERT: B 455 LEU cc_start: 0.8560 (tp) cc_final: 0.8268 (tt) REVERT: B 557 LYS cc_start: 0.9122 (mtmm) cc_final: 0.8808 (mtmt) REVERT: B 571 ASP cc_start: 0.8568 (t0) cc_final: 0.8061 (t0) REVERT: B 646 ARG cc_start: 0.9020 (tpp80) cc_final: 0.8645 (mmm160) REVERT: B 762 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7765 (mm110) REVERT: B 790 LYS cc_start: 0.8925 (mtmt) cc_final: 0.8699 (mmmm) REVERT: B 957 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: B 995 ARG cc_start: 0.8380 (mtt-85) cc_final: 0.8000 (mtt-85) outliers start: 109 outliers final: 64 residues processed: 556 average time/residue: 0.1982 time to fit residues: 171.6266 Evaluate side-chains 557 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 482 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 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 395 VAL Chi-restraints excluded: chain C residue 422 ASN 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 569 ILE Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 759 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 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 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 186 PHE 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 417 ASN Chi-restraints excluded: chain A residue 422 ASN 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 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 A residue 1148 PHE Chi-restraints excluded: chain B residue 87 ASN 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 422 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 661 GLU 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 957 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 282 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 196 optimal weight: 0.8980 chunk 305 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 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 66 HIS C 564 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 314 GLN A 354 ASN A 417 ASN A 613 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 121 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 804 GLN B1125 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.107123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085017 restraints weight = 61742.931| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.49 r_work: 0.3165 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 28623 Z= 0.171 Angle : 0.804 13.806 39132 Z= 0.375 Chirality : 0.050 0.498 4695 Planarity : 0.004 0.041 4842 Dihedral : 11.572 106.242 5886 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.68 % Allowed : 15.78 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3333 helix: 1.29 (0.20), residues: 774 sheet: 0.33 (0.19), residues: 654 loop : -1.11 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 237 TYR 0.019 0.001 TYR C1067 PHE 0.021 0.001 PHE B 338 TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00398 (28467) covalent geometry : angle 0.74949 (38709) SS BOND : bond 0.00590 ( 45) SS BOND : angle 2.77740 ( 90) hydrogen bonds : bond 0.04007 ( 1099) hydrogen bonds : angle 5.67421 ( 3000) link_ALPHA1-4 : bond 0.01682 ( 21) link_ALPHA1-4 : angle 2.88057 ( 63) link_BETA1-4 : bond 0.00255 ( 33) link_BETA1-4 : angle 1.51300 ( 99) link_BETA1-6 : bond 0.01388 ( 3) link_BETA1-6 : angle 2.53845 ( 9) link_NAG-ASN : bond 0.00536 ( 54) link_NAG-ASN : angle 3.56276 ( 162) *********************** 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 612 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 504 time to evaluate : 1.008 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: 0.8729 (mmmm) cc_final: 0.8285 (mmmm) REVERT: C 102 ARG cc_start: 0.7961 (mtt-85) cc_final: 0.7640 (mmt90) REVERT: C 129 LYS cc_start: 0.7918 (tttt) cc_final: 0.7686 (tmtt) REVERT: C 137 ASN cc_start: 0.8946 (m110) cc_final: 0.8713 (m-40) REVERT: C 191 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7990 (mt-10) REVERT: C 271 GLN cc_start: 0.8888 (mt0) cc_final: 0.8644 (mt0) REVERT: C 317 ASN cc_start: 0.8320 (m110) cc_final: 0.8095 (m110) REVERT: C 377 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.6376 (t80) REVERT: C 398 ASP cc_start: 0.7058 (m-30) cc_final: 0.6513 (t0) REVERT: C 558 LYS cc_start: 0.9091 (mptt) cc_final: 0.8861 (mmmm) REVERT: C 563 GLN cc_start: 0.7954 (mt0) cc_final: 0.7678 (mp10) REVERT: C 586 ASP cc_start: 0.8226 (m-30) cc_final: 0.7818 (m-30) REVERT: C 654 GLU cc_start: 0.8321 (tt0) cc_final: 0.7890 (tt0) REVERT: C 675 GLN cc_start: 0.7692 (pp30) cc_final: 0.7140 (pp30) REVERT: C 690 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7580 (mm-40) REVERT: C 762 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7757 (mm110) REVERT: C 811 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7866 (ttmm) REVERT: C 820 ASP cc_start: 0.8515 (t0) cc_final: 0.8125 (m-30) REVERT: C 977 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8167 (mp) REVERT: C 988 GLU cc_start: 0.7690 (pp20) cc_final: 0.7448 (pp20) REVERT: C 1072 GLU cc_start: 0.8852 (pm20) cc_final: 0.8591 (pm20) REVERT: C 1148 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.6134 (p90) REVERT: A 116 SER cc_start: 0.8706 (m) cc_final: 0.8423 (p) REVERT: A 129 LYS cc_start: 0.8037 (tttt) cc_final: 0.7687 (ptmm) REVERT: A 137 ASN cc_start: 0.8543 (m110) cc_final: 0.7991 (p0) REVERT: A 191 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7867 (mt-10) REVERT: A 287 ASP cc_start: 0.8496 (t0) cc_final: 0.8280 (t0) REVERT: A 377 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6558 (t80) REVERT: A 581 THR cc_start: 0.8772 (p) cc_final: 0.8315 (p) REVERT: A 583 GLU cc_start: 0.7946 (mp0) cc_final: 0.7618 (mp0) REVERT: A 586 ASP cc_start: 0.8317 (m-30) cc_final: 0.7924 (m-30) REVERT: A 654 GLU cc_start: 0.8425 (tt0) cc_final: 0.8027 (tt0) REVERT: A 675 GLN cc_start: 0.7495 (pp30) cc_final: 0.6774 (pp30) REVERT: A 690 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7723 (mm110) REVERT: A 737 ASP cc_start: 0.7634 (t0) cc_final: 0.7423 (t0) REVERT: A 755 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8501 (mp10) REVERT: A 776 LYS cc_start: 0.8923 (tttp) cc_final: 0.8643 (tttp) REVERT: A 790 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8725 (mtpp) REVERT: A 820 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8113 (m-30) REVERT: A 848 ASP cc_start: 0.7799 (t70) cc_final: 0.7535 (t0) REVERT: A 950 ASP cc_start: 0.8273 (m-30) cc_final: 0.7870 (m-30) REVERT: A 977 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 988 GLU cc_start: 0.7763 (pp20) cc_final: 0.7173 (pp20) REVERT: A 1005 GLN cc_start: 0.8638 (tp40) cc_final: 0.8321 (tp40) REVERT: A 1072 GLU cc_start: 0.8729 (pm20) cc_final: 0.8227 (pm20) REVERT: A 1125 ASN cc_start: 0.8709 (p0) cc_final: 0.8375 (p0) REVERT: B 41 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8397 (mmmm) REVERT: B 95 ILE cc_start: 0.9078 (mm) cc_final: 0.8818 (tp) REVERT: B 102 ARG cc_start: 0.7702 (mtt-85) cc_final: 0.7143 (mmt90) REVERT: B 121 ASN cc_start: 0.6820 (OUTLIER) cc_final: 0.6183 (t0) REVERT: B 129 LYS cc_start: 0.8154 (tttt) cc_final: 0.7924 (ptmm) REVERT: B 153 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5383 (tmm) REVERT: B 191 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 317 ASN cc_start: 0.8258 (m110) cc_final: 0.8020 (m110) REVERT: B 355 ARG cc_start: 0.8415 (ttt90) cc_final: 0.7950 (ttt90) REVERT: B 377 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6228 (t80) REVERT: B 390 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8782 (mp) REVERT: B 455 LEU cc_start: 0.8484 (tp) cc_final: 0.8220 (tt) REVERT: B 466 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6496 (ptp90) REVERT: B 557 LYS cc_start: 0.9115 (mtmm) cc_final: 0.8792 (mtmt) REVERT: B 571 ASP cc_start: 0.8535 (t0) cc_final: 0.8032 (t0) REVERT: B 646 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8581 (mmm160) REVERT: B 675 GLN cc_start: 0.7885 (pp30) cc_final: 0.7678 (tp40) REVERT: B 790 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8581 (mtmm) REVERT: B 811 LYS cc_start: 0.8379 (ttmm) cc_final: 0.7781 (ttmm) REVERT: B 814 LYS cc_start: 0.8899 (mptt) cc_final: 0.8484 (mmtt) REVERT: B 820 ASP cc_start: 0.8575 (t0) cc_final: 0.8190 (m-30) REVERT: B 957 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: B 995 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.7929 (mtt-85) outliers start: 108 outliers final: 74 residues processed: 564 average time/residue: 0.1938 time to fit residues: 170.6545 Evaluate side-chains 570 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 484 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 95 ILE 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 367 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 434 ILE 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 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 747 THR Chi-restraints excluded: chain C residue 759 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 984 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 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 350 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 385 THR 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 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 A residue 1148 PHE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 87 ASN 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 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 240 THR 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 569 ILE 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 957 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 7 optimal weight: 0.8980 chunk 170 optimal weight: 0.0870 chunk 332 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 188 optimal weight: 0.2980 chunk 196 optimal weight: 0.7980 chunk 324 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN A 314 GLN A 417 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 66 HIS B 121 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.108160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085926 restraints weight = 61999.456| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.57 r_work: 0.3178 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 28623 Z= 0.146 Angle : 0.789 13.298 39132 Z= 0.368 Chirality : 0.049 0.468 4695 Planarity : 0.004 0.040 4842 Dihedral : 11.115 105.341 5886 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.79 % Allowed : 17.42 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3333 helix: 1.41 (0.20), residues: 774 sheet: 0.37 (0.19), residues: 648 loop : -1.07 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.019 0.001 TYR C 351 PHE 0.022 0.001 PHE C 338 TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00335 (28467) covalent geometry : angle 0.73865 (38709) SS BOND : bond 0.00609 ( 45) SS BOND : angle 2.58306 ( 90) hydrogen bonds : bond 0.03746 ( 1099) hydrogen bonds : angle 5.58555 ( 3000) link_ALPHA1-4 : bond 0.01659 ( 21) link_ALPHA1-4 : angle 2.88107 ( 63) link_BETA1-4 : bond 0.00290 ( 33) link_BETA1-4 : angle 1.46398 ( 99) link_BETA1-6 : bond 0.01432 ( 3) link_BETA1-6 : angle 2.58051 ( 9) link_NAG-ASN : bond 0.00521 ( 54) link_NAG-ASN : angle 3.35378 ( 162) *********************** 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 579 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 497 time to evaluate : 1.078 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 32 PHE cc_start: 0.8513 (m-10) cc_final: 0.8249 (m-10) REVERT: C 41 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8296 (mmmm) REVERT: C 102 ARG cc_start: 0.7869 (mtt-85) cc_final: 0.7657 (mmt90) REVERT: C 129 LYS cc_start: 0.7898 (tttt) cc_final: 0.7657 (ptmm) REVERT: C 191 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8054 (mt-10) REVERT: C 271 GLN cc_start: 0.8893 (mt0) cc_final: 0.8621 (mt0) REVERT: C 377 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.6299 (t80) REVERT: C 398 ASP cc_start: 0.7078 (m-30) cc_final: 0.6544 (t0) REVERT: C 558 LYS cc_start: 0.9086 (mptt) cc_final: 0.8847 (mmmm) REVERT: C 563 GLN cc_start: 0.7922 (mt0) cc_final: 0.7669 (mp10) REVERT: C 586 ASP cc_start: 0.8219 (m-30) cc_final: 0.7823 (m-30) REVERT: C 649 CYS cc_start: 0.7062 (t) cc_final: 0.6640 (t) REVERT: C 654 GLU cc_start: 0.8358 (tt0) cc_final: 0.7925 (tt0) REVERT: C 675 GLN cc_start: 0.7693 (pp30) cc_final: 0.7131 (pp30) REVERT: C 690 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7583 (mm-40) REVERT: C 811 LYS cc_start: 0.8390 (ttmm) cc_final: 0.7885 (ttmm) REVERT: C 820 ASP cc_start: 0.8499 (t0) cc_final: 0.8119 (m-30) REVERT: C 977 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8170 (mp) REVERT: C 1072 GLU cc_start: 0.8862 (pm20) cc_final: 0.8591 (pm20) REVERT: C 1148 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.6193 (p90) REVERT: A 116 SER cc_start: 0.8690 (m) cc_final: 0.8397 (p) REVERT: A 129 LYS cc_start: 0.8020 (tttt) cc_final: 0.7639 (pttt) REVERT: A 137 ASN cc_start: 0.8530 (m110) cc_final: 0.8004 (p0) REVERT: A 191 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7801 (mt-10) REVERT: A 287 ASP cc_start: 0.8487 (t0) cc_final: 0.8256 (t0) REVERT: A 377 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6415 (t80) REVERT: A 581 THR cc_start: 0.8754 (p) cc_final: 0.8428 (p) REVERT: A 586 ASP cc_start: 0.8298 (m-30) cc_final: 0.7923 (m-30) REVERT: A 646 ARG cc_start: 0.8842 (mmm-85) cc_final: 0.8532 (mmm160) REVERT: A 654 GLU cc_start: 0.8482 (tt0) cc_final: 0.8084 (tt0) REVERT: A 675 GLN cc_start: 0.7504 (pp30) cc_final: 0.7075 (pp30) REVERT: A 737 ASP cc_start: 0.7318 (t0) cc_final: 0.7085 (t0) REVERT: A 755 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8480 (mp10) REVERT: A 776 LYS cc_start: 0.8906 (tttp) cc_final: 0.8667 (tttp) REVERT: A 790 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8706 (mtpp) REVERT: A 820 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: A 950 ASP cc_start: 0.8273 (m-30) cc_final: 0.7836 (m-30) REVERT: A 977 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 988 GLU cc_start: 0.7727 (pp20) cc_final: 0.7132 (pp20) REVERT: B 41 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8370 (mmmm) REVERT: B 95 ILE cc_start: 0.9029 (mm) cc_final: 0.8701 (tp) REVERT: B 121 ASN cc_start: 0.6899 (OUTLIER) cc_final: 0.6607 (t0) REVERT: B 129 LYS cc_start: 0.8131 (tttt) cc_final: 0.7798 (ptmm) REVERT: B 153 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.5319 (tmm) REVERT: B 191 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 317 ASN cc_start: 0.8281 (m110) cc_final: 0.8037 (m110) REVERT: B 355 ARG cc_start: 0.8423 (ttt90) cc_final: 0.7872 (ttt90) REVERT: B 377 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.6170 (t80) REVERT: B 390 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8730 (mp) REVERT: B 455 LEU cc_start: 0.8450 (tp) cc_final: 0.8208 (tt) REVERT: B 466 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6547 (ptp90) REVERT: B 560 LEU cc_start: 0.9107 (mt) cc_final: 0.8367 (mt) REVERT: B 563 GLN cc_start: 0.8064 (mt0) cc_final: 0.7798 (mp10) REVERT: B 571 ASP cc_start: 0.8546 (t0) cc_final: 0.8032 (t0) REVERT: B 586 ASP cc_start: 0.8280 (m-30) cc_final: 0.7872 (m-30) REVERT: B 646 ARG cc_start: 0.8957 (tpp80) cc_final: 0.8540 (mmm160) REVERT: B 790 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8630 (mtmm) REVERT: B 811 LYS cc_start: 0.8376 (ttmm) cc_final: 0.7882 (ttmm) REVERT: B 814 LYS cc_start: 0.8858 (mptt) cc_final: 0.8542 (mmtt) REVERT: B 820 ASP cc_start: 0.8573 (t0) cc_final: 0.8203 (m-30) REVERT: B 957 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8252 (tm-30) REVERT: B 995 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7865 (mtt-85) outliers start: 82 outliers final: 55 residues processed: 537 average time/residue: 0.2003 time to fit residues: 166.7929 Evaluate side-chains 540 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 473 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 VAL 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 367 VAL Chi-restraints excluded: chain C residue 377 PHE 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 524 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 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 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 422 ASN 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 860 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 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 30 ASN Chi-restraints excluded: chain B residue 121 ASN 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 240 THR 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 632 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 93 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 221 optimal weight: 0.5980 chunk 272 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 329 optimal weight: 0.7980 chunk 237 optimal weight: 0.6980 chunk 152 optimal weight: 0.0770 chunk 207 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 957 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 417 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 66 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 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 = 0.108516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086394 restraints weight = 61922.898| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.52 r_work: 0.3192 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28623 Z= 0.144 Angle : 0.785 13.419 39132 Z= 0.364 Chirality : 0.048 0.488 4695 Planarity : 0.004 0.041 4842 Dihedral : 10.571 104.456 5886 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.73 % Allowed : 17.66 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 3333 helix: 1.49 (0.20), residues: 774 sheet: 0.42 (0.19), residues: 648 loop : -1.05 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 237 TYR 0.017 0.001 TYR C1067 PHE 0.021 0.001 PHE B 168 TRP 0.018 0.001 TRP A 64 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00327 (28467) covalent geometry : angle 0.73790 (38709) SS BOND : bond 0.00532 ( 45) SS BOND : angle 2.38264 ( 90) hydrogen bonds : bond 0.03638 ( 1099) hydrogen bonds : angle 5.50174 ( 3000) link_ALPHA1-4 : bond 0.01662 ( 21) link_ALPHA1-4 : angle 2.91917 ( 63) link_BETA1-4 : bond 0.00301 ( 33) link_BETA1-4 : angle 1.44345 ( 99) link_BETA1-6 : bond 0.01514 ( 3) link_BETA1-6 : angle 2.66821 ( 9) link_NAG-ASN : bond 0.00490 ( 54) link_NAG-ASN : angle 3.23308 ( 162) *********************** 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 568 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 488 time to evaluate : 1.019 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 32 PHE cc_start: 0.8491 (m-10) cc_final: 0.8231 (m-10) REVERT: C 41 LYS cc_start: 0.8738 (mmmm) cc_final: 0.8371 (mmmm) REVERT: C 129 LYS cc_start: 0.7988 (tttt) cc_final: 0.7723 (ptmm) REVERT: C 191 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8056 (mt-10) REVERT: C 271 GLN cc_start: 0.8899 (mt0) cc_final: 0.8627 (mt0) REVERT: C 287 ASP cc_start: 0.8535 (t0) cc_final: 0.8316 (t0) REVERT: C 377 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6303 (t80) REVERT: C 398 ASP cc_start: 0.7082 (m-30) cc_final: 0.6556 (t0) REVERT: C 558 LYS cc_start: 0.9110 (mptt) cc_final: 0.8848 (mmmm) REVERT: C 563 GLN cc_start: 0.7939 (mt0) cc_final: 0.7685 (mp10) REVERT: C 586 ASP cc_start: 0.8196 (m-30) cc_final: 0.7810 (m-30) REVERT: C 649 CYS cc_start: 0.7073 (t) cc_final: 0.6672 (t) REVERT: C 654 GLU cc_start: 0.8356 (tt0) cc_final: 0.7926 (tt0) REVERT: C 675 GLN cc_start: 0.7683 (pp30) cc_final: 0.7101 (pp30) REVERT: C 690 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7615 (mm-40) REVERT: C 811 LYS cc_start: 0.8396 (ttmm) cc_final: 0.7901 (ttmm) REVERT: C 820 ASP cc_start: 0.8470 (t0) cc_final: 0.8080 (m-30) REVERT: C 859 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8568 (p) REVERT: C 977 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8167 (mp) REVERT: C 1072 GLU cc_start: 0.8859 (pm20) cc_final: 0.8587 (pm20) REVERT: C 1144 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8479 (mm-30) REVERT: C 1148 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.6298 (p90) REVERT: A 116 SER cc_start: 0.8674 (m) cc_final: 0.8346 (p) REVERT: A 129 LYS cc_start: 0.8006 (tttt) cc_final: 0.7651 (pttt) REVERT: A 137 ASN cc_start: 0.8463 (m110) cc_final: 0.7967 (p0) REVERT: A 191 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7834 (mt-10) REVERT: A 287 ASP cc_start: 0.8493 (t0) cc_final: 0.8267 (t0) REVERT: A 377 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6446 (t80) REVERT: A 581 THR cc_start: 0.8772 (p) cc_final: 0.8354 (p) REVERT: A 583 GLU cc_start: 0.7893 (mp0) cc_final: 0.7656 (mp0) REVERT: A 586 ASP cc_start: 0.8271 (m-30) cc_final: 0.7978 (m-30) REVERT: A 646 ARG cc_start: 0.8833 (mmm-85) cc_final: 0.8514 (mmm160) REVERT: A 654 GLU cc_start: 0.8449 (tt0) cc_final: 0.8051 (tt0) REVERT: A 675 GLN cc_start: 0.7484 (pp30) cc_final: 0.7061 (pp30) REVERT: A 755 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8483 (mp10) REVERT: A 780 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8423 (mt-10) REVERT: A 790 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8697 (mtpp) REVERT: A 820 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: A 950 ASP cc_start: 0.8264 (m-30) cc_final: 0.7842 (m-30) REVERT: A 977 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 988 GLU cc_start: 0.7724 (pp20) cc_final: 0.7161 (pp20) REVERT: B 41 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8309 (mmmm) REVERT: B 95 ILE cc_start: 0.8966 (mm) cc_final: 0.8760 (tp) REVERT: B 129 LYS cc_start: 0.8104 (tttt) cc_final: 0.7780 (ptmm) REVERT: B 153 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.5333 (tmm) REVERT: B 190 ARG cc_start: 0.8403 (mtt90) cc_final: 0.7156 (mpt90) REVERT: B 191 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7722 (mt-10) REVERT: B 317 ASN cc_start: 0.8246 (m110) cc_final: 0.7998 (m110) REVERT: B 355 ARG cc_start: 0.8426 (ttt90) cc_final: 0.8059 (ttt90) REVERT: B 377 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6177 (t80) REVERT: B 390 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8673 (mp) REVERT: B 455 LEU cc_start: 0.8462 (tp) cc_final: 0.8244 (tt) REVERT: B 563 GLN cc_start: 0.8040 (mt0) cc_final: 0.7798 (mp10) REVERT: B 571 ASP cc_start: 0.8513 (t0) cc_final: 0.7999 (t0) REVERT: B 646 ARG cc_start: 0.8936 (tpp80) cc_final: 0.8489 (mmm160) REVERT: B 790 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8726 (mtmm) REVERT: B 811 LYS cc_start: 0.8355 (ttmm) cc_final: 0.7885 (ttmm) REVERT: B 814 LYS cc_start: 0.8860 (mptt) cc_final: 0.8517 (mmtt) REVERT: B 820 ASP cc_start: 0.8580 (t0) cc_final: 0.8210 (m-30) REVERT: B 957 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: B 995 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7813 (mtt-85) REVERT: B 1127 ASP cc_start: 0.8430 (m-30) cc_final: 0.8229 (m-30) REVERT: B 1149 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7419 (tptp) outliers start: 80 outliers final: 54 residues processed: 527 average time/residue: 0.1958 time to fit residues: 161.7058 Evaluate side-chains 533 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 467 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 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 395 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 759 PHE 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 984 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 19 THR 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 417 ASN 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 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 30 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 240 THR 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 530 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 957 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 303 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 285 optimal weight: 0.8980 chunk 126 optimal weight: 0.0870 chunk 169 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 293 optimal weight: 0.8980 chunk 324 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 417 ASN A 762 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 66 HIS B 121 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.107450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085364 restraints weight = 62073.898| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.51 r_work: 0.3173 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 28623 Z= 0.187 Angle : 0.819 15.706 39132 Z= 0.381 Chirality : 0.049 0.480 4695 Planarity : 0.004 0.040 4842 Dihedral : 10.205 104.420 5886 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.42 % Allowed : 18.27 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3333 helix: 1.50 (0.20), residues: 774 sheet: 0.39 (0.19), residues: 648 loop : -1.08 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 765 TYR 0.027 0.002 TYR B 380 PHE 0.040 0.001 PHE C 133 TRP 0.015 0.001 TRP A 64 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00437 (28467) covalent geometry : angle 0.77161 (38709) SS BOND : bond 0.00561 ( 45) SS BOND : angle 2.72582 ( 90) hydrogen bonds : bond 0.03830 ( 1099) hydrogen bonds : angle 5.50224 ( 3000) link_ALPHA1-4 : bond 0.01778 ( 21) link_ALPHA1-4 : angle 3.00588 ( 63) link_BETA1-4 : bond 0.00226 ( 33) link_BETA1-4 : angle 1.44746 ( 99) link_BETA1-6 : bond 0.01600 ( 3) link_BETA1-6 : angle 2.74923 ( 9) link_NAG-ASN : bond 0.00481 ( 54) link_NAG-ASN : angle 3.24854 ( 162) ********************** 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 551 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 480 time to evaluate : 1.013 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: 0.8747 (mmmm) cc_final: 0.8374 (mmmm) REVERT: C 191 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8065 (mt-10) REVERT: C 287 ASP cc_start: 0.8534 (t0) cc_final: 0.8310 (t0) REVERT: C 377 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6404 (t80) REVERT: C 398 ASP cc_start: 0.7073 (m-30) cc_final: 0.6557 (t0) REVERT: C 558 LYS cc_start: 0.9119 (mptt) cc_final: 0.8855 (mmmm) REVERT: C 563 GLN cc_start: 0.7983 (mt0) cc_final: 0.7707 (mp10) REVERT: C 586 ASP cc_start: 0.8204 (m-30) cc_final: 0.7819 (m-30) REVERT: C 649 CYS cc_start: 0.6992 (t) cc_final: 0.6601 (t) REVERT: C 654 GLU cc_start: 0.8344 (tt0) cc_final: 0.7915 (tt0) REVERT: C 675 GLN cc_start: 0.7700 (pp30) cc_final: 0.7127 (pp30) REVERT: C 690 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7588 (mm-40) REVERT: C 811 LYS cc_start: 0.8416 (ttmm) cc_final: 0.7928 (ttmm) REVERT: C 820 ASP cc_start: 0.8492 (t0) cc_final: 0.8101 (m-30) REVERT: C 859 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8580 (p) REVERT: C 957 GLN cc_start: 0.8494 (tt0) cc_final: 0.8249 (tm-30) REVERT: C 977 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8200 (mp) REVERT: C 1072 GLU cc_start: 0.8865 (pm20) cc_final: 0.8580 (pm20) REVERT: C 1144 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8500 (mm-30) REVERT: A 116 SER cc_start: 0.8686 (m) cc_final: 0.8386 (p) REVERT: A 129 LYS cc_start: 0.8017 (tttt) cc_final: 0.7728 (ptmm) REVERT: A 137 ASN cc_start: 0.8510 (m110) cc_final: 0.8032 (p0) REVERT: A 191 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7852 (mt-10) REVERT: A 287 ASP cc_start: 0.8524 (t0) cc_final: 0.8304 (t0) REVERT: A 377 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6486 (t80) REVERT: A 581 THR cc_start: 0.8769 (p) cc_final: 0.8364 (p) REVERT: A 583 GLU cc_start: 0.7870 (mp0) cc_final: 0.7556 (mp0) REVERT: A 586 ASP cc_start: 0.8275 (m-30) cc_final: 0.7997 (m-30) REVERT: A 646 ARG cc_start: 0.8832 (mmm-85) cc_final: 0.8499 (mmm160) REVERT: A 654 GLU cc_start: 0.8443 (tt0) cc_final: 0.8109 (tt0) REVERT: A 675 GLN cc_start: 0.7523 (pp30) cc_final: 0.7091 (pp30) REVERT: A 755 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8485 (mp10) REVERT: A 776 LYS cc_start: 0.8891 (tttp) cc_final: 0.8651 (tttp) REVERT: A 790 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8721 (mtpp) REVERT: A 820 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: A 950 ASP cc_start: 0.8280 (m-30) cc_final: 0.7844 (m-30) REVERT: A 977 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 988 GLU cc_start: 0.7758 (pp20) cc_final: 0.7214 (pp20) REVERT: A 995 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8183 (mtm-85) REVERT: B 41 LYS cc_start: 0.8696 (mmmm) cc_final: 0.8286 (mmmm) REVERT: B 95 ILE cc_start: 0.8965 (mm) cc_final: 0.8682 (tp) REVERT: B 129 LYS cc_start: 0.8148 (tttt) cc_final: 0.7844 (ptmm) REVERT: B 153 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5309 (tmm) REVERT: B 190 ARG cc_start: 0.8361 (mtt90) cc_final: 0.7060 (mpt90) REVERT: B 191 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7734 (mt-10) REVERT: B 317 ASN cc_start: 0.8225 (m110) cc_final: 0.8002 (m110) REVERT: B 355 ARG cc_start: 0.8417 (ttt90) cc_final: 0.8036 (ttt90) REVERT: B 377 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.6218 (t80) REVERT: B 390 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8703 (mp) REVERT: B 455 LEU cc_start: 0.8491 (tp) cc_final: 0.8228 (tt) REVERT: B 563 GLN cc_start: 0.8092 (mt0) cc_final: 0.7784 (mp10) REVERT: B 571 ASP cc_start: 0.8531 (t0) cc_final: 0.8007 (t0) REVERT: B 646 ARG cc_start: 0.8928 (tpp80) cc_final: 0.8437 (mmm160) REVERT: B 773 GLU cc_start: 0.7845 (tt0) cc_final: 0.7617 (tt0) REVERT: B 790 LYS cc_start: 0.9025 (mtmt) cc_final: 0.8731 (mtmm) REVERT: B 811 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7942 (ttmm) REVERT: B 814 LYS cc_start: 0.8893 (mptt) cc_final: 0.8537 (mmtt) REVERT: B 820 ASP cc_start: 0.8575 (t0) cc_final: 0.8215 (m-30) REVERT: B 995 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.7888 (mtt-85) outliers start: 71 outliers final: 52 residues processed: 517 average time/residue: 0.1932 time to fit residues: 156.6158 Evaluate side-chains 532 residues out of total 2934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 471 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR 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 307 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 759 PHE 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 984 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 121 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 350 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 434 ILE 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 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 30 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 240 THR 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 530 SER Chi-restraints excluded: chain B residue 551 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 296 optimal weight: 0.0040 chunk 114 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 417 ASN A 519 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 66 HIS B 121 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.107692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085658 restraints weight = 61625.825| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.49 r_work: 0.3199 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3873 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= 0.167 Angle : 0.814 15.961 39132 Z= 0.379 Chirality : 0.049 0.463 4695 Planarity : 0.004 0.042 4842 Dihedral : 10.024 104.294 5886 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.28 % Allowed : 18.68 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3333 helix: 1.49 (0.20), residues: 774 sheet: 0.38 (0.19), residues: 648 loop : -1.07 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 765 TYR 0.043 0.002 TYR B 380 PHE 0.025 0.001 PHE C 133 TRP 0.014 0.001 TRP A 64 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00387 (28467) covalent geometry : angle 0.76819 (38709) SS BOND : bond 0.00544 ( 45) SS BOND : angle 2.54178 ( 90) hydrogen bonds : bond 0.03805 ( 1099) hydrogen bonds : angle 5.50312 ( 3000) link_ALPHA1-4 : bond 0.01778 ( 21) link_ALPHA1-4 : angle 3.00202 ( 63) link_BETA1-4 : bond 0.00265 ( 33) link_BETA1-4 : angle 1.44787 ( 99) link_BETA1-6 : bond 0.01661 ( 3) link_BETA1-6 : angle 2.74000 ( 9) link_NAG-ASN : bond 0.00461 ( 54) link_NAG-ASN : angle 3.20827 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7105.82 seconds wall clock time: 122 minutes 38.32 seconds (7358.32 seconds total)