Starting phenix.real_space_refine on Sun Jul 5 11:10:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e7b_30998/07_2026/7e7b_30998.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e7b_30998/07_2026/7e7b_30998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e7b_30998/07_2026/7e7b_30998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e7b_30998/07_2026/7e7b_30998.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e7b_30998/07_2026/7e7b_30998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e7b_30998/07_2026/7e7b_30998.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7e7b_30998/07_2026/7e7b_30998.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e7b_30998/07_2026/7e7b_30998.cif" } resolution = 2.6 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= 0.000 sd= 0.003 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 17370 2.51 5 N 4413 2.21 5 O 5460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27363 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 8613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8613 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 51, 'TRANS': 1050} Chain breaks: 3 Chain: "B" Number of atoms: 8613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8613 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 51, 'TRANS': 1050} Chain breaks: 3 Chain: "C" Number of atoms: 8613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8613 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 51, 'TRANS': 1050} 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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 chiralities: 2 Chain: "M" 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 chiralities: 2 Chain: "N" 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 chiralities: 2 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 chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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 chiralities: 2 Chain: "W" 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 chiralities: 2 Chain: "X" 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 chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" 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 chiralities: 2 Chain: "m" 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 chiralities: 2 Chain: "n" 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 chiralities: 2 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 chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Unusual residues: {'ELA': 2, 'NAG': 5, 'VCG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 132 Unusual residues: {'ELA': 1, 'NAG': 5, 'VCG': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 5.35, per 1000 atoms: 0.20 Number of scatterers: 27363 At special positions: 0 Unit cell: (146.745, 151.093, 177.181, 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 5460 8.00 N 4413 7.00 C 17370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 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 " " 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-ASN " NAG A1601 " - " ASN A 343 " " NAG A1602 " - " ASN A 331 " " NAG A1603 " - " ASN A 603 " " NAG A1604 " - " ASN A 657 " " NAG A1605 " - " ASN A 61 " " NAG B1601 " - " ASN B 343 " " NAG B1602 " - " ASN B 331 " " NAG B1603 " - " ASN B 603 " " NAG B1604 " - " ASN B 657 " " NAG B1605 " - " ASN B 61 " " NAG C1601 " - " ASN C 343 " " NAG C1602 " - " ASN C 331 " " NAG C1603 " - " ASN C 603 " " NAG C1604 " - " ASN C 657 " " NAG C1605 " - " ASN C 61 " " NAG D 1 " - " ASN A 616 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 149 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A 709 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A1074 " " NAG P 1 " - " ASN A 17 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN B 282 " " NAG V 1 " - " ASN B 234 " " NAG W 1 " - " ASN B 122 " " NAG X 1 " - " ASN B 149 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B 709 " " NAG a 1 " - " ASN B 165 " " NAG b 1 " - " ASN B1074 " " NAG c 1 " - " ASN B 17 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 717 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " " NAG h 1 " - " ASN C 282 " " NAG i 1 " - " ASN C 234 " " NAG j 1 " - " ASN C 122 " " NAG k 1 " - " ASN C 149 " " NAG l 1 " - " ASN C 801 " " NAG m 1 " - " ASN C 709 " " NAG n 1 " - " ASN C 165 " " NAG o 1 " - " ASN C1074 " " NAG p 1 " - " ASN C 17 " Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 853.4 milliseconds 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6180 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 54 sheets defined 25.1% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.830A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.722A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.624A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.871A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.091A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 987 through 1033 removed outlier: 4.159A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 4.193A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.832A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.723A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.624A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.871A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.090A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 987 through 1033 removed outlier: 4.159A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 4.192A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.833A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.722A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.624A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 848 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.871A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.090A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 987 through 1033 removed outlier: 4.159A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 4.193A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.979A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.979A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.854A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.975A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.574A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.522A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.673A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.418A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.199A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.914A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.317A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.898A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.898A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.445A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.628A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.980A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.980A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.854A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.974A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.575A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.523A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.674A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.417A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.212A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.701A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.318A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.898A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.898A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.356A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.980A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.980A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.853A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.974A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.574A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.523A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.672A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.417A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.212A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.771A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.317A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.898A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.898A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.355A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1122 1125 hydrogen bonds defined for protein. 3060 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4478 1.32 - 1.45: 8522 1.45 - 1.58: 14764 1.58 - 1.72: 7 1.72 - 1.85: 150 Bond restraints: 27921 Sorted by residual: bond pdb=" C27 VCG B1607 " pdb=" C28 VCG B1607 " ideal model delta sigma weight residual 1.527 1.216 0.311 2.00e-02 2.50e+03 2.43e+02 bond pdb=" C27 VCG A1608 " pdb=" C28 VCG A1608 " ideal model delta sigma weight residual 1.527 1.216 0.311 2.00e-02 2.50e+03 2.41e+02 bond pdb=" C27 VCG A1609 " pdb=" C28 VCG A1609 " ideal model delta sigma weight residual 1.527 1.217 0.310 2.00e-02 2.50e+03 2.41e+02 bond pdb=" C ELA A1607 " pdb=" OXT ELA A1607 " ideal model delta sigma weight residual 1.250 1.402 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" C ELA A1606 " pdb=" OXT ELA A1606 " ideal model delta sigma weight residual 1.250 1.402 -0.152 2.00e-02 2.50e+03 5.80e+01 ... (remaining 27916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 37558 3.61 - 7.23: 341 7.23 - 10.84: 31 10.84 - 14.46: 3 14.46 - 18.07: 2 Bond angle restraints: 37935 Sorted by residual: angle pdb=" N THR A 393 " pdb=" CA THR A 393 " pdb=" C THR A 393 " ideal model delta sigma weight residual 111.36 129.43 -18.07 1.09e+00 8.42e-01 2.75e+02 angle pdb=" N ASN A 149 " pdb=" CA ASN A 149 " pdb=" C ASN A 149 " ideal model delta sigma weight residual 114.04 99.53 14.51 1.24e+00 6.50e-01 1.37e+02 angle pdb=" N ASN B 282 " pdb=" CA ASN B 282 " pdb=" C ASN B 282 " ideal model delta sigma weight residual 109.63 97.93 11.70 1.49e+00 4.50e-01 6.17e+01 angle pdb=" N ASN A 282 " pdb=" CA ASN A 282 " pdb=" C ASN A 282 " ideal model delta sigma weight residual 109.63 98.24 11.39 1.49e+00 4.50e-01 5.84e+01 angle pdb=" N LEU B 441 " pdb=" CA LEU B 441 " pdb=" C LEU B 441 " ideal model delta sigma weight residual 111.36 119.61 -8.25 1.09e+00 8.42e-01 5.73e+01 ... (remaining 37930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.37: 15225 29.37 - 58.73: 655 58.73 - 88.10: 68 88.10 - 117.47: 10 117.47 - 146.83: 5 Dihedral angle restraints: 15963 sinusoidal: 6342 harmonic: 9621 Sorted by residual: dihedral pdb=" C THR A 393 " pdb=" N THR A 393 " pdb=" CA THR A 393 " pdb=" CB THR A 393 " ideal model delta harmonic sigma weight residual -122.00 -146.69 24.69 0 2.50e+00 1.60e-01 9.75e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.77 74.77 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.76 74.76 1 1.00e+01 1.00e-02 7.08e+01 ... (remaining 15960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 4473 0.194 - 0.388: 64 0.388 - 0.582: 4 0.582 - 0.776: 0 0.776 - 0.970: 1 Chirality restraints: 4542 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 1.03e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 9.86e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.19e+01 ... (remaining 4539 not shown) Planarity restraints: 4830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1601 " -0.360 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG B1601 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG B1601 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG B1601 " 0.550 2.00e-02 2.50e+03 pdb=" O7 NAG B1601 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1601 " -0.359 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C7 NAG C1601 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG C1601 " -0.130 2.00e-02 2.50e+03 pdb=" N2 NAG C1601 " 0.548 2.00e-02 2.50e+03 pdb=" O7 NAG C1601 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1601 " 0.338 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG A1601 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A1601 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A1601 " -0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A1601 " 0.085 2.00e-02 2.50e+03 ... (remaining 4827 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3436 2.74 - 3.28: 24881 3.28 - 3.82: 45870 3.82 - 4.36: 57661 4.36 - 4.90: 97374 Nonbonded interactions: 229222 Sorted by model distance: nonbonded pdb=" OG1 THR C 76 " pdb=" O TRP C 258 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 76 " pdb=" O TRP A 258 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR B 76 " pdb=" O TRP B 258 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASP A 843 " pdb=" NH1 ARG A 847 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASP C 843 " pdb=" NH1 ARG C 847 " model vdw 2.201 3.120 ... (remaining 229217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1605) selection = (chain 'B' and resid 14 through 1605) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } 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: 1.490 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: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.470 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 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 : 0.011 0.311 28059 Z= 0.524 Angle : 0.956 18.074 38304 Z= 0.527 Chirality : 0.067 0.970 4542 Planarity : 0.020 0.310 4776 Dihedral : 15.889 146.833 9648 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.49 % Allowed : 4.07 % Favored : 90.44 % Cbeta Deviations : 0.10 % 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: -2.02 (0.13), residues: 3282 helix: -1.24 (0.16), residues: 747 sheet: -0.22 (0.18), residues: 744 loop : -1.91 (0.12), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 765 TYR 0.018 0.002 TYR A 495 PHE 0.016 0.002 PHE A 133 TRP 0.017 0.002 TRP B 436 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.01083 / 0.52 (27921) covalent geometry : angle 0.92947 / 0.52 (37935) SS BOND : bond 0.01051 / 0.64 ( 45) SS BOND : angle 2.55653 / 1.90 ( 90) hydrogen bonds : bond 0.18246 / 12.19 ( 1095) hydrogen bonds : angle 8.17810 / 5.63 ( 3060) link_BETA1-4 : bond 0.00243 / 0.16 ( 39) link_BETA1-4 : angle 1.76190 / 1.16 ( 117) link_NAG-ASN : bond 0.00714 / 0.43 ( 54) link_NAG-ASN : angle 2.83910 / 1.78 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 289 time to evaluate : 1.066 Fit side-chains REVERT: A 14 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6858 (mp-120) REVERT: A 935 GLN cc_start: 0.8661 (tt0) cc_final: 0.8377 (tt0) REVERT: A 1029 MET cc_start: 0.8827 (tpp) cc_final: 0.8548 (tpp) REVERT: A 1138 TYR cc_start: 0.8461 (t80) cc_final: 0.8223 (t80) REVERT: A 1142 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7119 (tp40) REVERT: B 155 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8519 (p) REVERT: B 179 LEU cc_start: 0.8861 (mt) cc_final: 0.8645 (mt) REVERT: B 346 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7657 (mtp-110) REVERT: B 583 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: B 697 MET cc_start: 0.8718 (ptm) cc_final: 0.8329 (ptm) REVERT: B 935 GLN cc_start: 0.8676 (tt0) cc_final: 0.8439 (tt0) REVERT: C 14 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6881 (mp-120) REVERT: C 900 MET cc_start: 0.8788 (mtp) cc_final: 0.8530 (mtt) outliers start: 158 outliers final: 18 residues processed: 406 average time/residue: 0.6022 time to fit residues: 288.8035 Evaluate side-chains 170 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 115 GLN A 134 GLN A 314 GLN A 317 ASN A 474 GLN A 487 ASN A 607 GLN A 779 GLN A 901 GLN A 926 GLN B 30 ASN B 115 GLN B 314 GLN B 317 ASN B 474 GLN B 607 GLN B 675 GLN B 779 GLN B 901 GLN B 926 GLN B1002 GLN C 30 ASN C 115 GLN C 134 GLN C 317 ASN C 474 GLN C 487 ASN C 493 GLN C 607 GLN C 779 GLN C 901 GLN C 926 GLN C 935 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.085741 restraints weight = 38001.318| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.24 r_work: 0.2904 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28059 Z= 0.127 Angle : 0.616 10.458 38304 Z= 0.308 Chirality : 0.044 0.216 4542 Planarity : 0.004 0.030 4776 Dihedral : 10.637 124.670 3789 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.40 % Allowed : 9.49 % Favored : 88.11 % 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: -1.00 (0.14), residues: 3282 helix: 0.55 (0.19), residues: 735 sheet: -0.01 (0.18), residues: 789 loop : -1.53 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 847 TYR 0.013 0.001 TYR A1067 PHE 0.016 0.001 PHE A 392 TRP 0.009 0.001 TRP B 64 HIS 0.002 0.001 HIS C1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (27921) covalent geometry : angle 0.58584 / 0.30 (37935) SS BOND : bond 0.00346 / 0.21 ( 45) SS BOND : angle 1.45824 / 1.09 ( 90) hydrogen bonds : bond 0.04870 / 3.17 ( 1095) hydrogen bonds : angle 6.13458 / 4.23 ( 3060) link_BETA1-4 : bond 0.00395 / 0.25 ( 39) link_BETA1-4 : angle 1.54162 / 1.04 ( 117) link_NAG-ASN : bond 0.00410 / 0.25 ( 54) link_NAG-ASN : angle 2.56679 / 1.65 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 199 time to evaluate : 1.122 Fit side-chains REVERT: A 78 ARG cc_start: 0.7814 (mmp-170) cc_final: 0.7475 (mmm160) REVERT: A 169 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8337 (tm-30) REVERT: A 795 LYS cc_start: 0.6399 (mttt) cc_final: 0.6154 (mtpm) REVERT: A 935 GLN cc_start: 0.8845 (tt0) cc_final: 0.8445 (tt0) REVERT: A 1107 ARG cc_start: 0.8617 (mpt180) cc_final: 0.8383 (mtt90) REVERT: A 1138 TYR cc_start: 0.8253 (t80) cc_final: 0.7979 (t80) REVERT: B 346 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8331 (mtp-110) REVERT: B 487 ASN cc_start: 0.8539 (m110) cc_final: 0.8317 (m-40) REVERT: B 583 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8656 (pt0) REVERT: B 697 MET cc_start: 0.9161 (ptm) cc_final: 0.8957 (ptm) REVERT: B 795 LYS cc_start: 0.6495 (mttt) cc_final: 0.6227 (mtpm) REVERT: B 808 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6297 (m-30) REVERT: B 935 GLN cc_start: 0.8856 (tt0) cc_final: 0.8593 (tt0) REVERT: B 1038 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8520 (mmtp) REVERT: C 80 ASP cc_start: 0.8052 (m-30) cc_final: 0.7835 (m-30) REVERT: C 164 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7270 (p0) REVERT: C 493 GLN cc_start: 0.8498 (mt0) cc_final: 0.8234 (tt0) REVERT: C 528 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8749 (tttm) REVERT: C 529 LYS cc_start: 0.8460 (tmtm) cc_final: 0.8096 (mmmt) REVERT: C 900 MET cc_start: 0.8916 (mtp) cc_final: 0.8664 (mtt) REVERT: C 1038 LYS cc_start: 0.9030 (mptt) cc_final: 0.8823 (mmtp) outliers start: 69 outliers final: 21 residues processed: 248 average time/residue: 0.6564 time to fit residues: 191.5149 Evaluate side-chains 186 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 86 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 519 HIS A 675 GLN A 907 ASN A1002 GLN B 493 GLN B 519 HIS B1002 GLN C 280 ASN C 314 GLN C 519 HIS C 675 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.082949 restraints weight = 38061.055| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.25 r_work: 0.2854 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 28059 Z= 0.264 Angle : 0.661 8.334 38304 Z= 0.333 Chirality : 0.047 0.167 4542 Planarity : 0.004 0.031 4776 Dihedral : 9.439 112.213 3765 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.71 % Allowed : 9.94 % Favored : 87.35 % 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: -0.80 (0.14), residues: 3282 helix: 0.80 (0.19), residues: 717 sheet: 0.03 (0.18), residues: 798 loop : -1.39 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 847 TYR 0.018 0.002 TYR B 495 PHE 0.018 0.002 PHE A 392 TRP 0.010 0.002 TRP A 436 HIS 0.004 0.001 HIS C1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.26 (27921) covalent geometry : angle 0.63588 / 0.33 (37935) SS BOND : bond 0.00859 / 0.55 ( 45) SS BOND : angle 1.93616 / 1.49 ( 90) hydrogen bonds : bond 0.05676 / 3.69 ( 1095) hydrogen bonds : angle 6.12001 / 4.22 ( 3060) link_BETA1-4 : bond 0.00339 / 0.23 ( 39) link_BETA1-4 : angle 1.41569 / 0.96 ( 117) link_NAG-ASN : bond 0.00344 / 0.22 ( 54) link_NAG-ASN : angle 2.25264 / 1.48 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 174 time to evaluate : 1.095 Fit side-chains REVERT: A 78 ARG cc_start: 0.7793 (mmp-170) cc_final: 0.7492 (mmm160) REVERT: A 169 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8400 (tm-30) REVERT: A 935 GLN cc_start: 0.8870 (tt0) cc_final: 0.8503 (tt0) REVERT: A 1138 TYR cc_start: 0.8289 (t80) cc_final: 0.8077 (t80) REVERT: B 21 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8206 (mtm180) REVERT: B 145 TYR cc_start: 0.8930 (t80) cc_final: 0.8546 (t80) REVERT: B 153 MET cc_start: 0.8187 (mtm) cc_final: 0.7973 (mtm) REVERT: B 346 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.8338 (mtp-110) REVERT: B 808 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6263 (m-30) REVERT: B 935 GLN cc_start: 0.8901 (tt0) cc_final: 0.8633 (tt0) REVERT: B 1038 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8532 (mmtp) REVERT: C 80 ASP cc_start: 0.8144 (m-30) cc_final: 0.7849 (m-30) REVERT: C 211 ASN cc_start: 0.8871 (t0) cc_final: 0.8593 (t0) REVERT: C 516 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: C 528 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8864 (tttm) REVERT: C 900 MET cc_start: 0.8948 (mtp) cc_final: 0.8696 (mtt) REVERT: C 1005 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8565 (tp40) outliers start: 78 outliers final: 34 residues processed: 230 average time/residue: 0.6551 time to fit residues: 177.1838 Evaluate side-chains 199 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 129 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 156 optimal weight: 20.0000 chunk 296 optimal weight: 0.0570 chunk 271 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 69 HIS A 675 GLN A1002 GLN B 69 HIS B 675 GLN B1002 GLN C 69 HIS C 675 GLN C 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.115000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.086304 restraints weight = 37982.991| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.22 r_work: 0.2915 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28059 Z= 0.110 Angle : 0.538 7.682 38304 Z= 0.272 Chirality : 0.043 0.158 4542 Planarity : 0.003 0.030 4776 Dihedral : 8.326 99.676 3758 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.26 % Allowed : 11.23 % Favored : 86.51 % 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: -0.43 (0.14), residues: 3282 helix: 1.61 (0.20), residues: 675 sheet: 0.04 (0.17), residues: 807 loop : -1.22 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 847 TYR 0.015 0.001 TYR C1138 PHE 0.009 0.001 PHE A 133 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (27921) covalent geometry : angle 0.51698 / 0.27 (37935) SS BOND : bond 0.00409 / 0.28 ( 45) SS BOND : angle 1.36560 / 1.04 ( 90) hydrogen bonds : bond 0.04329 / 2.81 ( 1095) hydrogen bonds : angle 5.67678 / 3.91 ( 3060) link_BETA1-4 : bond 0.00363 / 0.23 ( 39) link_BETA1-4 : angle 1.25253 / 0.84 ( 117) link_NAG-ASN : bond 0.00219 / 0.14 ( 54) link_NAG-ASN : angle 1.93952 / 1.24 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8848 (m) cc_final: 0.8645 (p) REVERT: A 66 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7362 (p-80) REVERT: A 795 LYS cc_start: 0.6315 (mttt) cc_final: 0.6065 (mtpm) REVERT: A 935 GLN cc_start: 0.8856 (tt0) cc_final: 0.8512 (tt0) REVERT: A 1107 ARG cc_start: 0.8618 (mpt180) cc_final: 0.8382 (mpt180) REVERT: A 1138 TYR cc_start: 0.8172 (t80) cc_final: 0.7966 (t80) REVERT: B 21 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8023 (mtm180) REVERT: B 145 TYR cc_start: 0.8927 (t80) cc_final: 0.8604 (t80) REVERT: B 571 ASP cc_start: 0.8485 (m-30) cc_final: 0.8106 (t70) REVERT: B 697 MET cc_start: 0.9100 (ptm) cc_final: 0.8833 (ptm) REVERT: B 776 LYS cc_start: 0.9142 (tttm) cc_final: 0.8865 (tttp) REVERT: B 808 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6375 (m-30) REVERT: B 828 LEU cc_start: 0.8145 (mp) cc_final: 0.7942 (mm) REVERT: B 935 GLN cc_start: 0.8858 (tt0) cc_final: 0.8642 (tt0) REVERT: B 1038 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8461 (mmtp) REVERT: C 80 ASP cc_start: 0.7971 (m-30) cc_final: 0.7699 (m-30) REVERT: C 164 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7396 (p0) REVERT: C 211 ASN cc_start: 0.8843 (t0) cc_final: 0.8619 (t0) REVERT: C 528 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8850 (tttm) REVERT: C 529 LYS cc_start: 0.8429 (tmtm) cc_final: 0.8161 (mmmt) REVERT: C 900 MET cc_start: 0.8904 (mtp) cc_final: 0.8661 (mtt) REVERT: C 902 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8966 (tpt) REVERT: C 1005 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8573 (tp40) outliers start: 65 outliers final: 26 residues processed: 249 average time/residue: 0.6052 time to fit residues: 178.3151 Evaluate side-chains 205 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 143 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 309 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 275 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 245 optimal weight: 0.6980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 675 GLN A1002 GLN B 280 ASN B 675 GLN B1002 GLN B1010 GLN C 280 ASN C 675 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.083686 restraints weight = 37920.195| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.22 r_work: 0.2867 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 28059 Z= 0.231 Angle : 0.622 9.336 38304 Z= 0.313 Chirality : 0.046 0.157 4542 Planarity : 0.004 0.031 4776 Dihedral : 8.518 98.652 3758 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.75 % Allowed : 11.40 % Favored : 85.85 % 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: -0.50 (0.14), residues: 3282 helix: 1.20 (0.20), residues: 711 sheet: 0.05 (0.17), residues: 810 loop : -1.18 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 847 TYR 0.019 0.002 TYR C1138 PHE 0.016 0.002 PHE C 133 TRP 0.009 0.001 TRP A 436 HIS 0.027 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 (27921) covalent geometry : angle 0.59882 / 0.31 (37935) SS BOND : bond 0.00762 / 0.46 ( 45) SS BOND : angle 1.92008 / 1.48 ( 90) hydrogen bonds : bond 0.05220 / 3.38 ( 1095) hydrogen bonds : angle 5.85435 / 4.03 ( 3060) link_BETA1-4 : bond 0.00296 / 0.19 ( 39) link_BETA1-4 : angle 1.33768 / 0.90 ( 117) link_NAG-ASN : bond 0.00289 / 0.18 ( 54) link_NAG-ASN : angle 2.06282 / 1.35 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 182 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7977 (m-30) cc_final: 0.7633 (m-30) REVERT: A 169 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: A 935 GLN cc_start: 0.8918 (tt0) cc_final: 0.8579 (tt0) REVERT: A 1107 ARG cc_start: 0.8653 (mpt180) cc_final: 0.8430 (mpt180) REVERT: A 1138 TYR cc_start: 0.8250 (t80) cc_final: 0.8016 (t80) REVERT: B 21 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8305 (mtm180) REVERT: B 145 TYR cc_start: 0.8929 (t80) cc_final: 0.8566 (t80) REVERT: B 271 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8523 (mt0) REVERT: B 493 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: B 571 ASP cc_start: 0.8440 (m-30) cc_final: 0.8059 (t70) REVERT: B 808 ASP cc_start: 0.6446 (OUTLIER) cc_final: 0.6154 (m-30) REVERT: B 828 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7956 (mm) REVERT: B 935 GLN cc_start: 0.8877 (tt0) cc_final: 0.8613 (tt0) REVERT: B 1038 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8489 (mmtp) REVERT: B 1123 SER cc_start: 0.8953 (m) cc_final: 0.8556 (t) REVERT: C 80 ASP cc_start: 0.8118 (m-30) cc_final: 0.7772 (m-30) REVERT: C 164 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7390 (p0) REVERT: C 271 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8495 (mt0) REVERT: C 528 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8839 (tttm) REVERT: C 529 LYS cc_start: 0.8603 (tmtm) cc_final: 0.8114 (mmmm) REVERT: C 900 MET cc_start: 0.8955 (mtp) cc_final: 0.8680 (mtt) outliers start: 79 outliers final: 40 residues processed: 233 average time/residue: 0.5743 time to fit residues: 159.0182 Evaluate side-chains 220 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 310 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 303 optimal weight: 0.8980 chunk 214 optimal weight: 0.8980 chunk 282 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 280 ASN A 675 GLN A1002 GLN B 69 HIS B 280 ASN B 675 GLN B1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.086187 restraints weight = 37984.028| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.22 r_work: 0.2914 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28059 Z= 0.116 Angle : 0.536 9.302 38304 Z= 0.270 Chirality : 0.043 0.162 4542 Planarity : 0.003 0.035 4776 Dihedral : 7.776 91.833 3758 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.33 % Allowed : 12.10 % Favored : 85.58 % 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: -0.32 (0.14), residues: 3282 helix: 1.71 (0.20), residues: 690 sheet: 0.07 (0.17), residues: 822 loop : -1.16 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 847 TYR 0.019 0.001 TYR C1138 PHE 0.009 0.001 PHE C 238 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.000 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (27921) covalent geometry : angle 0.51529 / 0.26 (37935) SS BOND : bond 0.00382 / 0.25 ( 45) SS BOND : angle 1.39847 / 1.08 ( 90) hydrogen bonds : bond 0.04284 / 2.77 ( 1095) hydrogen bonds : angle 5.53791 / 3.81 ( 3060) link_BETA1-4 : bond 0.00356 / 0.23 ( 39) link_BETA1-4 : angle 1.25437 / 0.85 ( 117) link_NAG-ASN : bond 0.00209 / 0.13 ( 54) link_NAG-ASN : angle 1.87527 / 1.20 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 192 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7996 (m-30) cc_final: 0.7619 (m-30) REVERT: A 795 LYS cc_start: 0.6354 (mttt) cc_final: 0.6015 (mtpm) REVERT: A 935 GLN cc_start: 0.8851 (tt0) cc_final: 0.8500 (tt0) REVERT: A 1029 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8374 (tpp) REVERT: A 1138 TYR cc_start: 0.8161 (t80) cc_final: 0.7928 (t80) REVERT: B 21 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7993 (mtm180) REVERT: B 96 GLU cc_start: 0.7673 (pm20) cc_final: 0.7298 (pm20) REVERT: B 271 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8426 (mt0) REVERT: B 571 ASP cc_start: 0.8396 (m-30) cc_final: 0.8010 (t70) REVERT: B 786 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8046 (mmmt) REVERT: B 808 ASP cc_start: 0.6454 (OUTLIER) cc_final: 0.6124 (m-30) REVERT: B 935 GLN cc_start: 0.8849 (tt0) cc_final: 0.8614 (tt0) REVERT: B 1038 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8455 (mmtp) REVERT: B 1107 ARG cc_start: 0.8512 (mtt90) cc_final: 0.7901 (mtm-85) REVERT: C 80 ASP cc_start: 0.8014 (m-30) cc_final: 0.7685 (m-30) REVERT: C 96 GLU cc_start: 0.7378 (pm20) cc_final: 0.7067 (pm20) REVERT: C 118 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8933 (tp) REVERT: C 528 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8827 (tttm) REVERT: C 529 LYS cc_start: 0.8604 (tmtm) cc_final: 0.8208 (mmmt) REVERT: C 900 MET cc_start: 0.8922 (mtp) cc_final: 0.8684 (mtt) REVERT: C 902 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8963 (tpt) REVERT: C 1005 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8496 (tp40) outliers start: 67 outliers final: 33 residues processed: 234 average time/residue: 0.5886 time to fit residues: 163.6684 Evaluate side-chains 223 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 210 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 269 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 69 HIS A 675 GLN A1002 GLN B 69 HIS B 280 ASN B 498 GLN B 675 GLN B1002 GLN C 675 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.083672 restraints weight = 37651.525| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.22 r_work: 0.2869 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 28059 Z= 0.236 Angle : 0.621 9.150 38304 Z= 0.312 Chirality : 0.046 0.155 4542 Planarity : 0.004 0.031 4776 Dihedral : 7.911 92.656 3756 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.57 % Allowed : 11.92 % Favored : 85.51 % 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: -0.43 (0.14), residues: 3282 helix: 1.30 (0.20), residues: 711 sheet: 0.19 (0.17), residues: 795 loop : -1.21 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 847 TYR 0.020 0.002 TYR C1138 PHE 0.016 0.002 PHE C 133 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 (27921) covalent geometry : angle 0.59766 / 0.31 (37935) SS BOND : bond 0.00763 / 0.46 ( 45) SS BOND : angle 1.89177 / 1.45 ( 90) hydrogen bonds : bond 0.05185 / 3.35 ( 1095) hydrogen bonds : angle 5.79623 / 3.99 ( 3060) link_BETA1-4 : bond 0.00290 / 0.19 ( 39) link_BETA1-4 : angle 1.34094 / 0.91 ( 117) link_NAG-ASN : bond 0.00288 / 0.18 ( 54) link_NAG-ASN : angle 2.03637 / 1.34 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 181 time to evaluate : 0.893 Fit side-chains REVERT: A 80 ASP cc_start: 0.7992 (m-30) cc_final: 0.7669 (m-30) REVERT: B 21 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8064 (mtm180) REVERT: B 271 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8442 (mt0) REVERT: B 571 ASP cc_start: 0.8431 (m-30) cc_final: 0.8046 (t70) REVERT: B 786 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8049 (mmmt) REVERT: B 808 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.6101 (m-30) REVERT: B 935 GLN cc_start: 0.8866 (tt0) cc_final: 0.8609 (tt0) REVERT: B 1038 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8513 (mmtp) REVERT: C 80 ASP cc_start: 0.8058 (m-30) cc_final: 0.7713 (m-30) REVERT: C 118 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8928 (tp) REVERT: C 131 CYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6714 (m) REVERT: C 271 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8497 (mt0) REVERT: C 528 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8855 (tttm) REVERT: C 529 LYS cc_start: 0.8594 (tmtm) cc_final: 0.8237 (mmmt) REVERT: C 900 MET cc_start: 0.8975 (mtp) cc_final: 0.8702 (mtt) outliers start: 74 outliers final: 38 residues processed: 234 average time/residue: 0.5531 time to fit residues: 154.3730 Evaluate side-chains 219 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 288 optimal weight: 2.9990 chunk 280 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 300 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 320 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 69 HIS A 675 GLN A1002 GLN B 69 HIS B 280 ASN B 675 GLN B1002 GLN C 69 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.085362 restraints weight = 37890.708| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.23 r_work: 0.2898 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28059 Z= 0.142 Angle : 0.564 9.654 38304 Z= 0.283 Chirality : 0.043 0.169 4542 Planarity : 0.003 0.061 4776 Dihedral : 7.421 89.467 3756 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.19 % Allowed : 12.30 % Favored : 85.51 % 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: -0.31 (0.14), residues: 3282 helix: 1.63 (0.20), residues: 690 sheet: 0.16 (0.17), residues: 813 loop : -1.15 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 847 TYR 0.022 0.001 TYR A 904 PHE 0.012 0.001 PHE C 133 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (27921) covalent geometry : angle 0.54174 / 0.28 (37935) SS BOND : bond 0.00473 / 0.30 ( 45) SS BOND : angle 1.72155 / 1.36 ( 90) hydrogen bonds : bond 0.04540 / 2.94 ( 1095) hydrogen bonds : angle 5.60284 / 3.86 ( 3060) link_BETA1-4 : bond 0.00321 / 0.21 ( 39) link_BETA1-4 : angle 1.28360 / 0.87 ( 117) link_NAG-ASN : bond 0.00210 / 0.13 ( 54) link_NAG-ASN : angle 1.91206 / 1.23 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.7264 (p-80) REVERT: A 80 ASP cc_start: 0.7958 (m-30) cc_final: 0.7598 (m-30) REVERT: A 169 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: A 795 LYS cc_start: 0.6468 (mttt) cc_final: 0.6107 (mtpm) REVERT: A 935 GLN cc_start: 0.8856 (tt0) cc_final: 0.8496 (tt0) REVERT: A 1107 ARG cc_start: 0.8567 (mpt180) cc_final: 0.8326 (mmt90) REVERT: B 271 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8428 (mt0) REVERT: B 571 ASP cc_start: 0.8405 (m-30) cc_final: 0.8029 (t70) REVERT: B 786 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8088 (mmmt) REVERT: B 935 GLN cc_start: 0.8850 (tt0) cc_final: 0.8638 (tt0) REVERT: B 1038 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8481 (mmtp) REVERT: C 80 ASP cc_start: 0.8045 (m-30) cc_final: 0.7727 (m-30) REVERT: C 118 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8922 (tp) REVERT: C 271 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: C 528 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8845 (tttm) REVERT: C 529 LYS cc_start: 0.8616 (tmtm) cc_final: 0.8290 (mmmt) REVERT: C 900 MET cc_start: 0.8947 (mtp) cc_final: 0.8686 (mtt) REVERT: C 902 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8958 (tpt) REVERT: C 1005 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8507 (tp40) outliers start: 63 outliers final: 40 residues processed: 235 average time/residue: 0.5970 time to fit residues: 166.1212 Evaluate side-chains 225 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 111 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 328 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 199 optimal weight: 0.7980 chunk 329 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 69 HIS A 675 GLN A1002 GLN B 69 HIS B 317 ASN B 675 GLN B1002 GLN C 675 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.083440 restraints weight = 37918.036| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.23 r_work: 0.2864 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 28059 Z= 0.256 Angle : 0.648 9.992 38304 Z= 0.326 Chirality : 0.047 0.222 4542 Planarity : 0.004 0.064 4776 Dihedral : 7.670 90.294 3756 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.29 % Allowed : 12.48 % Favored : 85.23 % 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: -0.48 (0.14), residues: 3282 helix: 1.23 (0.19), residues: 711 sheet: 0.07 (0.17), residues: 819 loop : -1.18 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 847 TYR 0.023 0.002 TYR A 904 PHE 0.015 0.002 PHE A 133 TRP 0.010 0.001 TRP A 436 HIS 0.015 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.26 (27921) covalent geometry : angle 0.62236 / 0.32 (37935) SS BOND : bond 0.00823 / 0.50 ( 45) SS BOND : angle 2.24879 / 1.61 ( 90) hydrogen bonds : bond 0.05229 / 3.37 ( 1095) hydrogen bonds : angle 5.83429 / 4.01 ( 3060) link_BETA1-4 : bond 0.00278 / 0.18 ( 39) link_BETA1-4 : angle 1.40277 / 0.96 ( 117) link_NAG-ASN : bond 0.00371 / 0.26 ( 54) link_NAG-ASN : angle 2.07297 / 1.38 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7581 (p-80) REVERT: A 169 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: B 271 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8430 (mt0) REVERT: B 571 ASP cc_start: 0.8369 (m-30) cc_final: 0.8031 (t70) REVERT: B 786 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8065 (mmmt) REVERT: B 935 GLN cc_start: 0.8860 (tt0) cc_final: 0.8615 (tt0) REVERT: B 1038 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8514 (mmtp) REVERT: B 1123 SER cc_start: 0.8916 (m) cc_final: 0.8511 (t) REVERT: C 80 ASP cc_start: 0.8095 (m-30) cc_final: 0.7799 (m-30) REVERT: C 118 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8946 (tp) REVERT: C 271 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: C 528 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8844 (tttm) REVERT: C 529 LYS cc_start: 0.8578 (tmtm) cc_final: 0.8262 (mmmt) REVERT: C 900 MET cc_start: 0.8986 (mtp) cc_final: 0.8711 (mtt) REVERT: C 1005 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8563 (tp40) outliers start: 66 outliers final: 44 residues processed: 215 average time/residue: 0.5830 time to fit residues: 150.2305 Evaluate side-chains 220 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 220 optimal weight: 10.0000 chunk 275 optimal weight: 0.6980 chunk 311 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 323 optimal weight: 0.8980 chunk 232 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 69 HIS A 675 GLN A1002 GLN B 69 HIS B 317 ASN B 675 GLN B1002 GLN C 69 HIS C 764 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.086494 restraints weight = 37915.629| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.23 r_work: 0.2919 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28059 Z= 0.111 Angle : 0.546 10.098 38304 Z= 0.276 Chirality : 0.043 0.165 4542 Planarity : 0.004 0.073 4776 Dihedral : 7.129 86.263 3756 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.49 % Allowed : 13.38 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.14), residues: 3282 helix: 1.75 (0.20), residues: 690 sheet: 0.14 (0.17), residues: 822 loop : -1.14 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 847 TYR 0.024 0.001 TYR A 904 PHE 0.009 0.001 PHE C 238 TRP 0.011 0.001 TRP A 436 HIS 0.014 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (27921) covalent geometry : angle 0.52454 / 0.27 (37935) SS BOND : bond 0.00341 / 0.23 ( 45) SS BOND : angle 1.61777 / 1.17 ( 90) hydrogen bonds : bond 0.04160 / 2.69 ( 1095) hydrogen bonds : angle 5.50927 / 3.79 ( 3060) link_BETA1-4 : bond 0.00349 / 0.22 ( 39) link_BETA1-4 : angle 1.28218 / 0.87 ( 117) link_NAG-ASN : bond 0.00219 / 0.14 ( 54) link_NAG-ASN : angle 1.86453 / 1.21 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7319 (p-80) REVERT: A 795 LYS cc_start: 0.6451 (mttt) cc_final: 0.6106 (mtpm) REVERT: A 935 GLN cc_start: 0.8848 (tt0) cc_final: 0.8500 (tt0) REVERT: B 271 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8426 (mt0) REVERT: B 571 ASP cc_start: 0.8370 (m-30) cc_final: 0.8032 (t70) REVERT: B 786 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7927 (mmmt) REVERT: B 935 GLN cc_start: 0.8845 (tt0) cc_final: 0.8633 (tt0) REVERT: B 1038 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8461 (mmtp) REVERT: C 80 ASP cc_start: 0.8065 (m-30) cc_final: 0.7725 (m-30) REVERT: C 118 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8941 (tp) REVERT: C 144 TYR cc_start: 0.8830 (t80) cc_final: 0.8550 (t80) REVERT: C 176 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7868 (mm) REVERT: C 271 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8476 (mt0) REVERT: C 528 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8819 (tttm) REVERT: C 529 LYS cc_start: 0.8623 (tmtm) cc_final: 0.8311 (mmmt) REVERT: C 900 MET cc_start: 0.8952 (mtp) cc_final: 0.8707 (mtt) REVERT: C 902 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8946 (tpt) REVERT: C 1005 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8503 (tp40) outliers start: 43 outliers final: 33 residues processed: 219 average time/residue: 0.5556 time to fit residues: 146.9181 Evaluate side-chains 216 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 158 optimal weight: 0.0470 chunk 178 optimal weight: 0.2980 chunk 264 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 69 HIS A 675 GLN A1002 GLN B 69 HIS B 675 GLN B1002 GLN C 675 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.085273 restraints weight = 37771.100| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.21 r_work: 0.2898 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28059 Z= 0.172 Angle : 0.581 9.892 38304 Z= 0.293 Chirality : 0.044 0.213 4542 Planarity : 0.004 0.070 4776 Dihedral : 7.173 85.149 3756 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.63 % Allowed : 13.38 % Favored : 84.98 % 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: -0.28 (0.14), residues: 3282 helix: 1.70 (0.20), residues: 690 sheet: 0.12 (0.17), residues: 828 loop : -1.13 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 847 TYR 0.029 0.001 TYR B 904 PHE 0.012 0.001 PHE C 133 TRP 0.011 0.001 TRP B 152 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (27921) covalent geometry : angle 0.55631 / 0.29 (37935) SS BOND : bond 0.00572 / 0.36 ( 45) SS BOND : angle 2.06539 / 1.38 ( 90) hydrogen bonds : bond 0.04549 / 2.95 ( 1095) hydrogen bonds : angle 5.62023 / 3.86 ( 3060) link_BETA1-4 : bond 0.00295 / 0.19 ( 39) link_BETA1-4 : angle 1.29646 / 0.88 ( 117) link_NAG-ASN : bond 0.00266 / 0.18 ( 54) link_NAG-ASN : angle 1.91754 / 1.27 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9599.78 seconds wall clock time: 164 minutes 24.76 seconds (9864.76 seconds total)