Starting phenix.real_space_refine on Fri Jan 16 08:46:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lyo_63513/01_2026/9lyo_63513.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lyo_63513/01_2026/9lyo_63513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lyo_63513/01_2026/9lyo_63513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lyo_63513/01_2026/9lyo_63513.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lyo_63513/01_2026/9lyo_63513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lyo_63513/01_2026/9lyo_63513.map" } resolution = 3.07 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= 0.002 sd= 0.045 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 147 5.16 5 C 22054 2.51 5 N 5696 2.21 5 O 6937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34834 Number of models: 1 Model: "" Number of chains: 43 Chain: "i" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1639 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "j" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1674 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain: "A" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7992 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 7 Chain: "B" Number of atoms: 7933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7933 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 51, 'TRANS': 964} Chain breaks: 7 Chain: "C" Number of atoms: 7878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7878 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 8 Chain: "g" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1639 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 207} Chain: "h" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1674 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "l" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1639 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 207} Chain: "n" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1674 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 8.46, per 1000 atoms: 0.24 Number of scatterers: 34834 At special positions: 0 Unit cell: (172.98, 207.39, 236.22, 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 147 16.00 O 6937 8.00 N 5696 7.00 C 22054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS i 22 " - pdb=" SG CYS i 90 " distance=2.04 Simple disulfide: pdb=" SG CYS i 138 " - pdb=" SG CYS i 198 " distance=2.04 Simple disulfide: pdb=" SG CYS i 218 " - pdb=" SG CYS j 223 " distance=2.03 Simple disulfide: pdb=" SG CYS j 22 " - pdb=" SG CYS j 96 " distance=2.04 Simple disulfide: pdb=" SG CYS j 147 " - pdb=" SG CYS j 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 166 " distance=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.03 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 C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS g 22 " - pdb=" SG CYS g 90 " distance=2.03 Simple disulfide: pdb=" SG CYS g 138 " - pdb=" SG CYS g 198 " distance=2.03 Simple disulfide: pdb=" SG CYS g 218 " - pdb=" SG CYS h 223 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS h 147 " - pdb=" SG CYS h 203 " distance=2.03 Simple disulfide: pdb=" SG CYS l 22 " - pdb=" SG CYS l 90 " distance=2.03 Simple disulfide: pdb=" SG CYS l 138 " - pdb=" SG CYS l 198 " distance=2.03 Simple disulfide: pdb=" SG CYS l 218 " - pdb=" SG CYS n 223 " distance=2.03 Simple disulfide: pdb=" SG CYS n 22 " - pdb=" SG CYS n 96 " distance=2.03 Simple disulfide: pdb=" SG CYS n 147 " - pdb=" SG CYS n 203 " 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 k 1 " - " NAG k 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A1301 " - " ASN A 64 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 603 " " NAG B1301 " - " ASN B 64 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 657 " " NAG C1301 " - " ASN C 64 " " NAG C1302 " - " ASN C 123 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " " NAG D 1 " - " ASN A 123 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 616 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 123 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 709 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1074 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 282 " " NAG Z 1 " - " ASN C 331 " " NAG a 1 " - " ASN C 343 " " NAG b 1 " - " ASN C 616 " " NAG c 1 " - " ASN C 709 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1074 " " NAG k 1 " - " ASN C1098 " " NAG m 1 " - " ASN C1134 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.5 seconds 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8122 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 83 sheets defined 21.3% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'i' and resid 51 through 55 Processing helix chain 'i' and resid 124 through 132 Processing helix chain 'i' and resid 186 through 193 Processing helix chain 'i' and resid 216 through 218 No H-bonds generated for 'chain 'i' and resid 216 through 218' Processing helix chain 'j' and resid 87 through 91 removed outlier: 3.743A pdb=" N THR j 91 " --> pdb=" O THR j 88 " (cutoff:3.500A) Processing helix chain 'j' and resid 163 through 166 Processing helix chain 'j' and resid 193 through 197 removed outlier: 3.630A pdb=" N GLY j 197 " --> pdb=" O SER j 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 193 through 197' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.658A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.587A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.520A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 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 616 through 620 removed outlier: 3.598A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.573A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.662A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) 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 985 through 1033 removed outlier: 3.660A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.067A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.791A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.690A pdb=" N TYR B 505 " --> pdb=" O TYR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.828A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.526A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.609A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.544A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.809A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 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 removed outlier: 3.819A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.110A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.919A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.618A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.701A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.725A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.142A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 912 through 919' Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.563A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.067A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 4.210A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 85 Processing helix chain 'g' and resid 125 through 132 Processing helix chain 'g' and resid 187 through 193 removed outlier: 3.523A pdb=" N HIS g 193 " --> pdb=" O ASP g 189 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 32 Processing helix chain 'h' and resid 163 through 165 No H-bonds generated for 'chain 'h' and resid 163 through 165' Processing helix chain 'h' and resid 208 through 211 Processing helix chain 'l' and resid 25 through 32 removed outlier: 4.176A pdb=" N TYR l 32 " --> pdb=" O ASP l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 81 through 85 Processing helix chain 'l' and resid 125 through 132 Processing helix chain 'l' and resid 187 through 193 Processing helix chain 'l' and resid 216 through 218 No H-bonds generated for 'chain 'l' and resid 216 through 218' Processing helix chain 'n' and resid 87 through 91 Processing helix chain 'n' and resid 163 through 167 removed outlier: 3.754A pdb=" N THR n 167 " --> pdb=" O GLY n 164 " (cutoff:3.500A) Processing helix chain 'n' and resid 194 through 196 No H-bonds generated for 'chain 'n' and resid 194 through 196' Processing sheet with id=AA1, first strand: chain 'i' and resid 9 through 12 removed outlier: 6.515A pdb=" N VAL i 10 " --> pdb=" O THR i 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'i' and resid 17 through 23 Processing sheet with id=AA3, first strand: chain 'i' and resid 47 through 50 removed outlier: 6.325A pdb=" N TRP i 37 " --> pdb=" O MET i 49 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP i 87 " --> pdb=" O GLN i 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 118 through 122 removed outlier: 4.710A pdb=" N SER i 135 " --> pdb=" O LEU i 185 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU i 185 " --> pdb=" O SER i 135 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL i 137 " --> pdb=" O LEU i 183 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU i 183 " --> pdb=" O VAL i 137 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU i 139 " --> pdb=" O SER i 181 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER i 181 " --> pdb=" O LEU i 139 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN i 141 " --> pdb=" O LEU i 179 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU i 179 " --> pdb=" O ASN i 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'i' and resid 157 through 159 removed outlier: 4.164A pdb=" N TRP i 152 " --> pdb=" O GLN i 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'j' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'j' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'j' and resid 58 through 60 removed outlier: 5.368A pdb=" N TRP j 47 " --> pdb=" O ARG j 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG j 38 " --> pdb=" O TRP j 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'j' and resid 58 through 60 removed outlier: 5.368A pdb=" N TRP j 47 " --> pdb=" O ARG j 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG j 38 " --> pdb=" O TRP j 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'j' and resid 127 through 130 removed outlier: 3.853A pdb=" N SER j 127 " --> pdb=" O LYS j 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'j' and resid 158 through 161 removed outlier: 4.412A pdb=" N TYR j 201 " --> pdb=" O VAL j 218 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N HIS j 207 " --> pdb=" O THR j 212 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR j 212 " --> pdb=" O HIS j 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'j' and resid 176 through 177 Processing sheet with id=AB4, first strand: chain 'A' and resid 32 through 34 removed outlier: 8.188A pdb=" N ASN A 64 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR A 269 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 94 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL A 39 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AB6, first strand: chain 'A' and resid 51 through 58 removed outlier: 3.736A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.896A pdb=" N GLY A 104 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 168 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AB9, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AC1, first strand: chain 'A' and resid 324 through 327 removed outlier: 3.808A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.627A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.635A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.861A pdb=" N PHE A 565 " --> pdb=" O PHE B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.482A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD1, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.081A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.376A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.376A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'B' and resid 31 through 34 removed outlier: 7.853A pdb=" N ASN B 64 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR B 269 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 265 " --> pdb=" O PHE B 68 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 31 through 34 removed outlier: 7.853A pdb=" N ASN B 64 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR B 269 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 265 " --> pdb=" O PHE B 68 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 51 through 58 removed outlier: 3.789A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.507A pdb=" N VAL B 121 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 134 through 136 removed outlier: 4.085A pdb=" N SER B 162 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.529A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AE3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.931A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.777A pdb=" N PHE B 565 " --> pdb=" O PHE C 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.844A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.552A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 714 through 728 removed outlier: 6.560A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.396A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1076 through 1077 Processing sheet with id=AF2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.723A pdb=" N SER C 63 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASN C 64 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR C 269 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 188 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 51 through 58 removed outlier: 3.509A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.646A pdb=" N PHE C 168 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.558A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.773A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.629A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.693A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AG3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.019A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.343A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.405A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.512A pdb=" N LYS C1086 " --> pdb=" O HIS C1083 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG8, first strand: chain 'g' and resid 9 through 12 removed outlier: 4.317A pdb=" N ASP g 87 " --> pdb=" O GLN g 40 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN g 40 " --> pdb=" O ASP g 87 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 9 through 12 Processing sheet with id=AH1, first strand: chain 'g' and resid 18 through 23 Processing sheet with id=AH2, first strand: chain 'g' and resid 118 through 122 removed outlier: 5.573A pdb=" N TYR g 177 " --> pdb=" O ASN g 142 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'g' and resid 157 through 159 removed outlier: 4.440A pdb=" N TRP g 152 " --> pdb=" O GLN g 159 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'h' and resid 3 through 7 Processing sheet with id=AH5, first strand: chain 'h' and resid 11 through 12 removed outlier: 7.033A pdb=" N MET h 34 " --> pdb=" O VAL h 50 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'h' and resid 11 through 12 removed outlier: 3.622A pdb=" N SER h 98 " --> pdb=" O TYR h 109 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR h 109 " --> pdb=" O SER h 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 128 through 131 Processing sheet with id=AH8, first strand: chain 'h' and resid 158 through 161 removed outlier: 4.065A pdb=" N TYR h 201 " --> pdb=" O VAL h 218 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'h' and resid 176 through 177 Processing sheet with id=AI1, first strand: chain 'l' and resid 9 through 12 removed outlier: 3.552A pdb=" N GLY l 12 " --> pdb=" O THR l 108 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER l 36 " --> pdb=" O ASN l 91 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'l' and resid 9 through 12 removed outlier: 3.552A pdb=" N GLY l 12 " --> pdb=" O THR l 108 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'l' and resid 17 through 23 Processing sheet with id=AI4, first strand: chain 'l' and resid 118 through 122 removed outlier: 3.783A pdb=" N SER l 118 " --> pdb=" O ASN l 141 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR l 177 " --> pdb=" O ASN l 142 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'l' and resid 157 through 158 Processing sheet with id=AI6, first strand: chain 'n' and resid 3 through 7 Processing sheet with id=AI7, first strand: chain 'n' and resid 11 through 12 removed outlier: 6.871A pdb=" N MET n 34 " --> pdb=" O VAL n 50 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL n 50 " --> pdb=" O MET n 34 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TRP n 36 " --> pdb=" O VAL n 48 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'n' and resid 11 through 12 Processing sheet with id=AI9, first strand: chain 'n' and resid 128 through 131 removed outlier: 3.625A pdb=" N LEU n 185 " --> pdb=" O VAL n 149 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'n' and resid 128 through 131 removed outlier: 3.625A pdb=" N LEU n 185 " --> pdb=" O VAL n 149 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'n' and resid 158 through 161 removed outlier: 3.869A pdb=" N TYR n 201 " --> pdb=" O VAL n 218 " (cutoff:3.500A) 1447 hydrogen bonds defined for protein. 3861 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: 10.08 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10964 1.34 - 1.46: 8867 1.46 - 1.59: 15584 1.59 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 35595 Sorted by residual: bond pdb=" N VAL B 524 " pdb=" CA VAL B 524 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.83e+00 bond pdb=" N ASN B 334 " pdb=" CA ASN B 334 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.16e-02 7.43e+03 6.72e+00 bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.514 1.501 0.013 5.50e-03 3.31e+04 5.84e+00 bond pdb=" CA SER B 530 " pdb=" CB SER B 530 " ideal model delta sigma weight residual 1.530 1.495 0.034 1.48e-02 4.57e+03 5.40e+00 ... (remaining 35590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 46023 1.46 - 2.92: 2031 2.92 - 4.37: 329 4.37 - 5.83: 32 5.83 - 7.29: 13 Bond angle restraints: 48428 Sorted by residual: angle pdb=" N GLY j 113 " pdb=" CA GLY j 113 " pdb=" C GLY j 113 " ideal model delta sigma weight residual 111.93 118.90 -6.97 1.15e+00 7.56e-01 3.67e+01 angle pdb=" CA PHE B 392 " pdb=" C PHE B 392 " pdb=" O PHE B 392 " ideal model delta sigma weight residual 120.32 114.56 5.76 1.10e+00 8.26e-01 2.74e+01 angle pdb=" C ALA C 846 " pdb=" CA ALA C 846 " pdb=" CB ALA C 846 " ideal model delta sigma weight residual 117.23 110.98 6.25 1.36e+00 5.41e-01 2.11e+01 angle pdb=" N ASP A 89 " pdb=" CA ASP A 89 " pdb=" C ASP A 89 " ideal model delta sigma weight residual 114.75 109.95 4.80 1.26e+00 6.30e-01 1.45e+01 angle pdb=" N ASN i 141 " pdb=" CA ASN i 141 " pdb=" C ASN i 141 " ideal model delta sigma weight residual 109.40 115.21 -5.81 1.63e+00 3.76e-01 1.27e+01 ... (remaining 48423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 20696 17.89 - 35.78: 1194 35.78 - 53.67: 232 53.67 - 71.56: 64 71.56 - 89.45: 34 Dihedral angle restraints: 22220 sinusoidal: 9551 harmonic: 12669 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -28.97 -57.03 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 149.31 -56.31 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 42.35 50.65 1 1.00e+01 1.00e-02 3.51e+01 ... (remaining 22217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4956 0.069 - 0.139: 733 0.139 - 0.208: 21 0.208 - 0.278: 4 0.278 - 0.347: 4 Chirality restraints: 5718 Sorted by residual: chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.32e+00 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 7.25e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 5715 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.011 2.00e-02 2.50e+03 3.50e-02 2.45e+01 pdb=" CG TYR B 495 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.036 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 523 " -0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C THR B 523 " 0.075 2.00e-02 2.50e+03 pdb=" O THR B 523 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL B 524 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 389 " -0.021 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C ASP B 389 " 0.075 2.00e-02 2.50e+03 pdb=" O ASP B 389 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU B 390 " -0.026 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 619 2.66 - 3.22: 34597 3.22 - 3.78: 51046 3.78 - 4.34: 72685 4.34 - 4.90: 121089 Nonbonded interactions: 280036 Sorted by model distance: nonbonded pdb=" O3 NAG M 1 " pdb=" O7 NAG M 1 " model vdw 2.099 3.040 nonbonded pdb=" O ILE g 96 " pdb=" OG SER g 97 " model vdw 2.116 3.040 nonbonded pdb=" O3 NAG P 1 " pdb=" O7 NAG P 1 " model vdw 2.150 3.040 nonbonded pdb=" O3 NAG B1305 " pdb=" O7 NAG B1305 " model vdw 2.154 3.040 nonbonded pdb=" O SER i 82 " pdb=" OE1 GLU i 85 " model vdw 2.197 3.040 ... (remaining 280031 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 30 through 142 or resid 155 through 211 or resid 217 throu \ gh 243 or resid 264 through 621 or resid 641 through 675 or resid 691 through 11 \ 46 or resid 1301 through 1305)) selection = (chain 'B' and (resid 30 through 142 or resid 155 through 211 or resid 217 throu \ gh 621 or resid 641 through 1146 or resid 1302 through 1306)) selection = (chain 'C' and (resid 30 through 827 or resid 845 through 1305)) } 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 'k' selection = chain 'm' } ncs_group { reference = chain 'g' selection = chain 'i' selection = chain 'l' } ncs_group { reference = chain 'h' selection = chain 'j' selection = chain 'n' } 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: 3.960 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.850 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.060 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 : 0.005 0.048 35725 Z= 0.229 Angle : 0.719 14.357 48765 Z= 0.391 Chirality : 0.047 0.347 5718 Planarity : 0.005 0.113 6146 Dihedral : 12.342 89.454 13939 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.17 % Favored : 93.55 % Rotamer: Outliers : 0.08 % Allowed : 0.29 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % 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: -0.21 (0.13), residues: 4309 helix: 1.45 (0.20), residues: 708 sheet: 0.81 (0.14), residues: 1253 loop : -1.23 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 355 TYR 0.065 0.002 TYR B 495 PHE 0.025 0.002 PHE B 906 TRP 0.027 0.002 TRP j 110 HIS 0.015 0.001 HIS j 171 Details of bonding type rmsd covalent geometry : bond 0.00471 (35595) covalent geometry : angle 0.68670 (48428) SS BOND : bond 0.00415 ( 53) SS BOND : angle 1.42422 ( 106) hydrogen bonds : bond 0.20422 ( 1376) hydrogen bonds : angle 8.60224 ( 3861) link_BETA1-4 : bond 0.00678 ( 31) link_BETA1-4 : angle 3.22858 ( 93) link_NAG-ASN : bond 0.00586 ( 46) link_NAG-ASN : angle 2.89982 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 319 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 LYS cc_start: 0.6733 (tttt) cc_final: 0.6381 (ttpp) REVERT: B 448 ASN cc_start: 0.5552 (t0) cc_final: 0.5246 (m-40) REVERT: C 134 PHE cc_start: 0.7659 (m-80) cc_final: 0.7273 (m-80) REVERT: C 515 PHE cc_start: 0.6222 (p90) cc_final: 0.5634 (p90) REVERT: C 817 PHE cc_start: 0.7378 (t80) cc_final: 0.7030 (t80) REVERT: C 858 LEU cc_start: 0.9036 (tt) cc_final: 0.8628 (mp) REVERT: g 51 TYR cc_start: 0.7554 (p90) cc_final: 0.7253 (p90) REVERT: g 84 ASP cc_start: 0.2991 (m-30) cc_final: 0.2760 (m-30) REVERT: g 85 GLU cc_start: 0.6002 (tm-30) cc_final: 0.5562 (mt-10) REVERT: g 177 TYR cc_start: 0.4058 (m-80) cc_final: 0.3804 (m-80) REVERT: l 49 MET cc_start: 0.3710 (mpp) cc_final: 0.2676 (mpp) outliers start: 3 outliers final: 2 residues processed: 322 average time/residue: 0.2373 time to fit residues: 122.0202 Evaluate side-chains 155 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 30.0000 chunk 155 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 360 ASN C 388 ASN C 703 ASN l 202 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.143492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.104678 restraints weight = 126416.128| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 6.41 r_work: 0.3196 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35725 Z= 0.235 Angle : 0.737 16.224 48765 Z= 0.373 Chirality : 0.049 0.363 5718 Planarity : 0.005 0.077 6146 Dihedral : 7.050 56.221 6328 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.38 % Favored : 94.43 % Rotamer: Outliers : 1.08 % Allowed : 5.23 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % 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: -0.14 (0.13), residues: 4309 helix: 1.60 (0.19), residues: 697 sheet: 0.69 (0.14), residues: 1278 loop : -1.12 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1039 TYR 0.027 0.002 TYR B 873 PHE 0.034 0.002 PHE j 129 TRP 0.029 0.002 TRP l 37 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00546 (35595) covalent geometry : angle 0.70726 (48428) SS BOND : bond 0.00807 ( 53) SS BOND : angle 2.08463 ( 106) hydrogen bonds : bond 0.05277 ( 1376) hydrogen bonds : angle 6.37694 ( 3861) link_BETA1-4 : bond 0.00469 ( 31) link_BETA1-4 : angle 2.54291 ( 93) link_NAG-ASN : bond 0.00504 ( 46) link_NAG-ASN : angle 2.93796 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: A 1050 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.7529 (ppp) REVERT: B 130 LYS cc_start: 0.7331 (tttt) cc_final: 0.6827 (tmmt) REVERT: C 207 HIS cc_start: 0.6943 (t70) cc_final: 0.6687 (t-90) REVERT: C 347 PHE cc_start: 0.5878 (m-80) cc_final: 0.4094 (m-80) REVERT: C 858 LEU cc_start: 0.9101 (tt) cc_final: 0.8654 (mp) REVERT: g 84 ASP cc_start: 0.3029 (m-30) cc_final: 0.2772 (m-30) REVERT: l 64 PHE cc_start: 0.4281 (m-80) cc_final: 0.3520 (m-10) REVERT: n 34 MET cc_start: 0.2297 (mmt) cc_final: 0.1564 (mmm) outliers start: 41 outliers final: 19 residues processed: 201 average time/residue: 0.2118 time to fit residues: 71.2084 Evaluate side-chains 151 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1118 HIS Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain l residue 50 ILE Chi-restraints excluded: chain l residue 150 VAL Chi-restraints excluded: chain n residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 231 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 321 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 413 optimal weight: 50.0000 chunk 218 optimal weight: 0.0980 chunk 83 optimal weight: 7.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 31 ASN A 207 HIS A 317 ASN A 787 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1002 GLN C 360 ASN C 703 ASN C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.143359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.105318 restraints weight = 126271.589| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 7.69 r_work: 0.3177 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35725 Z= 0.196 Angle : 0.668 10.800 48765 Z= 0.336 Chirality : 0.046 0.326 5718 Planarity : 0.004 0.079 6146 Dihedral : 6.816 56.613 6328 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 1.29 % Allowed : 8.00 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.11 (0.13), residues: 4309 helix: 1.71 (0.19), residues: 696 sheet: 0.65 (0.14), residues: 1298 loop : -1.10 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG j 87 TYR 0.024 0.002 TYR g 51 PHE 0.030 0.002 PHE j 173 TRP 0.041 0.002 TRP l 37 HIS 0.008 0.001 HIS i 193 Details of bonding type rmsd covalent geometry : bond 0.00456 (35595) covalent geometry : angle 0.64457 (48428) SS BOND : bond 0.00332 ( 53) SS BOND : angle 1.27953 ( 106) hydrogen bonds : bond 0.04435 ( 1376) hydrogen bonds : angle 5.93918 ( 3861) link_BETA1-4 : bond 0.00564 ( 31) link_BETA1-4 : angle 2.42809 ( 93) link_NAG-ASN : bond 0.00462 ( 46) link_NAG-ASN : angle 2.62236 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 99 TRP cc_start: 0.7781 (m-90) cc_final: 0.7460 (m-90) REVERT: A 239 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: A 934 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9034 (tp) REVERT: B 189 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8759 (mt) REVERT: B 423 TYR cc_start: 0.7260 (t80) cc_final: 0.7041 (t80) REVERT: C 207 HIS cc_start: 0.7013 (t70) cc_final: 0.6730 (t-90) REVERT: C 347 PHE cc_start: 0.5733 (m-80) cc_final: 0.4168 (m-80) REVERT: C 858 LEU cc_start: 0.9127 (tt) cc_final: 0.8660 (mp) REVERT: g 84 ASP cc_start: 0.3177 (m-30) cc_final: 0.2802 (m-30) REVERT: g 85 GLU cc_start: 0.5271 (tm-30) cc_final: 0.4759 (mt-10) REVERT: g 143 PHE cc_start: 0.2639 (p90) cc_final: 0.2353 (p90) REVERT: n 34 MET cc_start: 0.2300 (mmt) cc_final: 0.2011 (mmt) outliers start: 49 outliers final: 27 residues processed: 185 average time/residue: 0.2014 time to fit residues: 63.9928 Evaluate side-chains 151 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1118 HIS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain n residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 381 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 314 optimal weight: 0.1980 chunk 110 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 chunk 413 optimal weight: 50.0000 chunk 402 optimal weight: 9.9990 chunk 8 optimal weight: 40.0000 chunk 344 optimal weight: 0.9980 chunk 300 optimal weight: 5.9990 chunk 353 optimal weight: 50.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.144451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.106189 restraints weight = 126484.106| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 7.46 r_work: 0.3192 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35725 Z= 0.115 Angle : 0.612 14.629 48765 Z= 0.306 Chirality : 0.045 0.313 5718 Planarity : 0.004 0.077 6146 Dihedral : 6.512 55.881 6326 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.76 % Favored : 95.08 % Rotamer: Outliers : 1.32 % Allowed : 8.93 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % 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: 0.05 (0.13), residues: 4309 helix: 1.91 (0.20), residues: 696 sheet: 0.75 (0.14), residues: 1315 loop : -1.03 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 19 TYR 0.027 0.001 TYR g 51 PHE 0.028 0.001 PHE B 486 TRP 0.034 0.001 TRP l 37 HIS 0.004 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00248 (35595) covalent geometry : angle 0.58960 (48428) SS BOND : bond 0.00250 ( 53) SS BOND : angle 1.04495 ( 106) hydrogen bonds : bond 0.03798 ( 1376) hydrogen bonds : angle 5.61876 ( 3861) link_BETA1-4 : bond 0.00620 ( 31) link_BETA1-4 : angle 2.32581 ( 93) link_NAG-ASN : bond 0.00392 ( 46) link_NAG-ASN : angle 2.41899 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 99 TRP cc_start: 0.7958 (m-90) cc_final: 0.7530 (m-90) REVERT: A 1050 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.7340 (ppp) REVERT: B 170 TYR cc_start: 0.7783 (t80) cc_final: 0.7460 (t80) REVERT: C 858 LEU cc_start: 0.9059 (tt) cc_final: 0.8602 (mp) REVERT: C 1118 HIS cc_start: 0.8581 (OUTLIER) cc_final: 0.8285 (t-170) REVERT: g 84 ASP cc_start: 0.2774 (m-30) cc_final: 0.2495 (m-30) REVERT: g 85 GLU cc_start: 0.4973 (tm-30) cc_final: 0.4679 (mt-10) REVERT: g 99 TRP cc_start: 0.5762 (m-90) cc_final: 0.5095 (m100) REVERT: g 143 PHE cc_start: 0.2913 (p90) cc_final: 0.2584 (p90) REVERT: h 34 MET cc_start: 0.1606 (mmt) cc_final: 0.1274 (mmp) REVERT: l 37 TRP cc_start: 0.3278 (t60) cc_final: 0.1781 (m100) REVERT: n 34 MET cc_start: 0.2005 (mmt) cc_final: 0.1796 (mmt) outliers start: 50 outliers final: 28 residues processed: 177 average time/residue: 0.2124 time to fit residues: 63.8056 Evaluate side-chains 149 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1118 HIS Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 1118 HIS Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 90 CYS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain l residue 50 ILE Chi-restraints excluded: chain n residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 132 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 413 optimal weight: 20.0000 chunk 306 optimal weight: 4.9990 chunk 295 optimal weight: 0.0970 chunk 199 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 703 ASN h 178 GLN l 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.143171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.104030 restraints weight = 125500.958| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 8.22 r_work: 0.3155 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35725 Z= 0.173 Angle : 0.628 10.016 48765 Z= 0.314 Chirality : 0.045 0.313 5718 Planarity : 0.004 0.078 6146 Dihedral : 6.479 56.178 6326 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.34 % Favored : 94.48 % Rotamer: Outliers : 1.80 % Allowed : 9.82 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % 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: 0.06 (0.13), residues: 4309 helix: 1.79 (0.19), residues: 701 sheet: 0.72 (0.14), residues: 1319 loop : -0.95 (0.13), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG h 38 TYR 0.029 0.002 TYR g 51 PHE 0.017 0.002 PHE h 29 TRP 0.034 0.002 TRP n 47 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00398 (35595) covalent geometry : angle 0.60496 (48428) SS BOND : bond 0.00352 ( 53) SS BOND : angle 1.21972 ( 106) hydrogen bonds : bond 0.03988 ( 1376) hydrogen bonds : angle 5.52687 ( 3861) link_BETA1-4 : bond 0.00540 ( 31) link_BETA1-4 : angle 2.31310 ( 93) link_NAG-ASN : bond 0.00468 ( 46) link_NAG-ASN : angle 2.50796 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 128 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: j 54 ASP cc_start: 0.7476 (p0) cc_final: 0.7234 (p0) REVERT: A 619 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: A 1050 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.7644 (ptp) REVERT: B 170 TYR cc_start: 0.7868 (t80) cc_final: 0.7623 (t80) REVERT: B 449 TYR cc_start: 0.7769 (m-80) cc_final: 0.7565 (m-80) REVERT: B 453 TYR cc_start: 0.7849 (p90) cc_final: 0.7466 (p90) REVERT: B 784 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: C 347 PHE cc_start: 0.6024 (m-80) cc_final: 0.4342 (m-80) REVERT: C 858 LEU cc_start: 0.9159 (tt) cc_final: 0.8617 (mp) REVERT: C 1118 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.8377 (t-170) REVERT: g 84 ASP cc_start: 0.3119 (m-30) cc_final: 0.2752 (m-30) REVERT: g 85 GLU cc_start: 0.5026 (tm-30) cc_final: 0.4645 (mt-10) REVERT: g 99 TRP cc_start: 0.5940 (m-90) cc_final: 0.5716 (m-90) REVERT: g 143 PHE cc_start: 0.2890 (p90) cc_final: 0.2575 (p90) REVERT: l 37 TRP cc_start: 0.3473 (t-100) cc_final: 0.2135 (m100) outliers start: 68 outliers final: 38 residues processed: 188 average time/residue: 0.2022 time to fit residues: 65.8070 Evaluate side-chains 159 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1118 HIS Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1118 HIS Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 90 CYS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain l residue 50 ILE Chi-restraints excluded: chain n residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 95 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 337 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 288 optimal weight: 20.0000 chunk 82 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 31 ASN j 206 ASN A 657 ASN A 901 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN n 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.143829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.104186 restraints weight = 126183.322| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 7.90 r_work: 0.3210 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35725 Z= 0.124 Angle : 0.582 10.117 48765 Z= 0.291 Chirality : 0.044 0.296 5718 Planarity : 0.004 0.077 6146 Dihedral : 6.323 55.762 6326 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.87 % Favored : 94.94 % Rotamer: Outliers : 1.40 % Allowed : 10.75 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % 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: 0.15 (0.13), residues: 4309 helix: 1.94 (0.19), residues: 699 sheet: 0.71 (0.14), residues: 1323 loop : -0.89 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG j 19 TYR 0.024 0.001 TYR g 51 PHE 0.031 0.001 PHE B 486 TRP 0.024 0.001 TRP i 99 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00276 (35595) covalent geometry : angle 0.56052 (48428) SS BOND : bond 0.00228 ( 53) SS BOND : angle 1.08781 ( 106) hydrogen bonds : bond 0.03625 ( 1376) hydrogen bonds : angle 5.35461 ( 3861) link_BETA1-4 : bond 0.00577 ( 31) link_BETA1-4 : angle 2.22248 ( 93) link_NAG-ASN : bond 0.00356 ( 46) link_NAG-ASN : angle 2.30167 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 110 LEU cc_start: 0.5762 (tp) cc_final: 0.5428 (mt) REVERT: j 54 ASP cc_start: 0.7449 (p0) cc_final: 0.7210 (p0) REVERT: A 214 ARG cc_start: 0.8175 (mmp-170) cc_final: 0.7951 (tpt90) REVERT: A 543 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: A 1050 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.7297 (ppp) REVERT: B 386 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7957 (mmmm) REVERT: B 449 TYR cc_start: 0.7700 (m-80) cc_final: 0.7488 (m-80) REVERT: C 342 PHE cc_start: 0.7959 (m-80) cc_final: 0.7562 (m-80) REVERT: C 347 PHE cc_start: 0.5843 (m-80) cc_final: 0.4040 (m-80) REVERT: C 858 LEU cc_start: 0.9114 (tt) cc_final: 0.8600 (mp) REVERT: C 1118 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.8218 (t-170) REVERT: g 84 ASP cc_start: 0.3323 (m-30) cc_final: 0.2944 (m-30) REVERT: g 85 GLU cc_start: 0.5018 (tm-30) cc_final: 0.4731 (mt-10) REVERT: g 99 TRP cc_start: 0.5709 (m-90) cc_final: 0.5416 (m-90) REVERT: g 143 PHE cc_start: 0.2920 (p90) cc_final: 0.2643 (p90) outliers start: 53 outliers final: 36 residues processed: 182 average time/residue: 0.2136 time to fit residues: 65.4613 Evaluate side-chains 164 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1118 HIS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1118 HIS Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 90 CYS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain l residue 50 ILE Chi-restraints excluded: chain n residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 206 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 384 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 152 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 406 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 chunk 259 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 142 ASN j 31 ASN j 74 ASN A 907 ASN B 207 HIS ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 913 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.127348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.078577 restraints weight = 117938.126| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 5.04 r_work: 0.3065 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 35725 Z= 0.342 Angle : 0.752 10.948 48765 Z= 0.375 Chirality : 0.050 0.333 5718 Planarity : 0.005 0.081 6146 Dihedral : 6.956 57.634 6326 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.22 % Favored : 93.57 % Rotamer: Outliers : 2.03 % Allowed : 10.96 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % 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: -0.17 (0.13), residues: 4309 helix: 1.41 (0.19), residues: 704 sheet: 0.50 (0.14), residues: 1322 loop : -0.99 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1039 TYR 0.027 0.002 TYR g 51 PHE 0.022 0.002 PHE B 93 TRP 0.043 0.003 TRP l 37 HIS 0.008 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00806 (35595) covalent geometry : angle 0.72811 (48428) SS BOND : bond 0.00504 ( 53) SS BOND : angle 1.51225 ( 106) hydrogen bonds : bond 0.04740 ( 1376) hydrogen bonds : angle 5.77765 ( 3861) link_BETA1-4 : bond 0.00476 ( 31) link_BETA1-4 : angle 2.45065 ( 93) link_NAG-ASN : bond 0.00761 ( 46) link_NAG-ASN : angle 2.86970 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 120 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 110 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5158 (mt) REVERT: j 54 ASP cc_start: 0.7622 (p0) cc_final: 0.7313 (p0) REVERT: A 619 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8085 (pm20) REVERT: A 1050 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8743 (ptm) REVERT: B 341 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8268 (p) REVERT: B 449 TYR cc_start: 0.7822 (m-80) cc_final: 0.7608 (m-80) REVERT: B 584 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7676 (pt) REVERT: B 784 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7913 (mt0) REVERT: C 342 PHE cc_start: 0.7954 (m-80) cc_final: 0.7577 (m-80) REVERT: C 858 LEU cc_start: 0.9119 (tt) cc_final: 0.8416 (mp) REVERT: g 84 ASP cc_start: 0.3104 (m-30) cc_final: 0.2710 (m-30) REVERT: g 85 GLU cc_start: 0.4954 (tm-30) cc_final: 0.4563 (mt-10) REVERT: g 99 TRP cc_start: 0.5615 (m-90) cc_final: 0.5276 (m-90) outliers start: 77 outliers final: 52 residues processed: 188 average time/residue: 0.1981 time to fit residues: 64.6967 Evaluate side-chains 167 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 109 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1118 HIS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1118 HIS Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 90 CYS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain l residue 50 ILE Chi-restraints excluded: chain l residue 58 SER Chi-restraints excluded: chain n residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 181 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 335 optimal weight: 0.6980 chunk 316 optimal weight: 0.9980 chunk 405 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 417 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 195 optimal weight: 0.0060 chunk 246 optimal weight: 0.0030 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN n 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.143646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.106794 restraints weight = 126266.023| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 8.22 r_work: 0.3169 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35725 Z= 0.106 Angle : 0.597 10.393 48765 Z= 0.297 Chirality : 0.044 0.299 5718 Planarity : 0.004 0.077 6146 Dihedral : 6.458 56.300 6326 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 1.51 % Allowed : 11.78 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % 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: 0.06 (0.13), residues: 4309 helix: 1.95 (0.19), residues: 690 sheet: 0.59 (0.14), residues: 1338 loop : -0.92 (0.13), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG j 19 TYR 0.025 0.001 TYR g 51 PHE 0.034 0.001 PHE B 486 TRP 0.052 0.002 TRP l 37 HIS 0.014 0.001 HIS j 207 Details of bonding type rmsd covalent geometry : bond 0.00223 (35595) covalent geometry : angle 0.57655 (48428) SS BOND : bond 0.00224 ( 53) SS BOND : angle 1.11900 ( 106) hydrogen bonds : bond 0.03657 ( 1376) hydrogen bonds : angle 5.31297 ( 3861) link_BETA1-4 : bond 0.00611 ( 31) link_BETA1-4 : angle 2.20303 ( 93) link_NAG-ASN : bond 0.00384 ( 46) link_NAG-ASN : angle 2.29132 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 64 PHE cc_start: 0.5389 (m-80) cc_final: 0.5091 (m-80) REVERT: i 110 LEU cc_start: 0.5862 (tp) cc_final: 0.5537 (mt) REVERT: j 19 ARG cc_start: 0.6551 (ttm-80) cc_final: 0.5681 (tpt90) REVERT: j 54 ASP cc_start: 0.7494 (p0) cc_final: 0.7229 (p0) REVERT: A 543 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: A 619 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: A 1050 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.7409 (ptp) REVERT: B 130 LYS cc_start: 0.7116 (tttt) cc_final: 0.6351 (tmmt) REVERT: B 386 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8348 (mmmm) REVERT: B 449 TYR cc_start: 0.7609 (m-80) cc_final: 0.7376 (m-80) REVERT: B 584 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7511 (pt) REVERT: B 784 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: C 342 PHE cc_start: 0.7979 (m-80) cc_final: 0.7682 (m-80) REVERT: C 858 LEU cc_start: 0.9062 (tt) cc_final: 0.8455 (mp) REVERT: g 84 ASP cc_start: 0.3448 (m-30) cc_final: 0.2982 (m-30) REVERT: g 85 GLU cc_start: 0.4965 (tm-30) cc_final: 0.4640 (mt-10) REVERT: g 99 TRP cc_start: 0.5580 (m-90) cc_final: 0.5267 (m-90) REVERT: g 143 PHE cc_start: 0.2315 (p90) cc_final: 0.2093 (p90) REVERT: n 185 LEU cc_start: 0.1675 (OUTLIER) cc_final: 0.1105 (tt) outliers start: 57 outliers final: 39 residues processed: 174 average time/residue: 0.2069 time to fit residues: 61.4536 Evaluate side-chains 163 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1118 HIS Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1118 HIS Chi-restraints excluded: chain g residue 18 ILE Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 90 CYS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain l residue 50 ILE Chi-restraints excluded: chain l residue 96 ILE Chi-restraints excluded: chain n residue 83 MET Chi-restraints excluded: chain n residue 185 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 301 optimal weight: 0.9980 chunk 407 optimal weight: 50.0000 chunk 361 optimal weight: 50.0000 chunk 41 optimal weight: 40.0000 chunk 35 optimal weight: 50.0000 chunk 45 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 198 optimal weight: 0.3980 chunk 327 optimal weight: 0.9990 chunk 167 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.143816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.106467 restraints weight = 125808.779| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 7.94 r_work: 0.3201 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 35725 Z= 0.107 Angle : 0.576 10.043 48765 Z= 0.287 Chirality : 0.043 0.284 5718 Planarity : 0.004 0.076 6146 Dihedral : 6.199 55.925 6326 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.13 % Favored : 94.76 % Rotamer: Outliers : 1.51 % Allowed : 11.94 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % 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: 0.21 (0.13), residues: 4309 helix: 2.08 (0.20), residues: 694 sheet: 0.70 (0.14), residues: 1332 loop : -0.84 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 237 TYR 0.027 0.001 TYR g 51 PHE 0.016 0.001 PHE B 157 TRP 0.051 0.002 TRP l 37 HIS 0.004 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00230 (35595) covalent geometry : angle 0.55578 (48428) SS BOND : bond 0.00209 ( 53) SS BOND : angle 1.05108 ( 106) hydrogen bonds : bond 0.03451 ( 1376) hydrogen bonds : angle 5.12428 ( 3861) link_BETA1-4 : bond 0.00620 ( 31) link_BETA1-4 : angle 2.15939 ( 93) link_NAG-ASN : bond 0.00346 ( 46) link_NAG-ASN : angle 2.22243 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 121 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 110 LEU cc_start: 0.5757 (tp) cc_final: 0.5444 (mt) REVERT: j 19 ARG cc_start: 0.6577 (ttm-80) cc_final: 0.5574 (tpt170) REVERT: j 54 ASP cc_start: 0.7432 (p0) cc_final: 0.7178 (p0) REVERT: A 206 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7810 (tmtt) REVERT: A 619 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: A 1050 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.7277 (ppp) REVERT: B 130 LYS cc_start: 0.7068 (tttt) cc_final: 0.6310 (tmmt) REVERT: B 386 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8173 (mmmm) REVERT: B 449 TYR cc_start: 0.7549 (m-80) cc_final: 0.7306 (m-80) REVERT: B 584 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7518 (pt) REVERT: B 784 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7662 (mt0) REVERT: C 342 PHE cc_start: 0.7981 (m-80) cc_final: 0.7654 (m-80) REVERT: C 858 LEU cc_start: 0.9086 (tt) cc_final: 0.8491 (mp) REVERT: g 84 ASP cc_start: 0.3552 (m-30) cc_final: 0.3095 (m-30) REVERT: g 85 GLU cc_start: 0.5000 (tm-30) cc_final: 0.4701 (mt-10) REVERT: g 99 TRP cc_start: 0.5567 (m-90) cc_final: 0.5207 (m-90) REVERT: g 143 PHE cc_start: 0.2154 (p90) cc_final: 0.1949 (p90) REVERT: n 185 LEU cc_start: 0.1663 (OUTLIER) cc_final: 0.1115 (tt) outliers start: 57 outliers final: 40 residues processed: 169 average time/residue: 0.2067 time to fit residues: 59.3674 Evaluate side-chains 161 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1118 HIS Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1118 HIS Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 90 CYS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain l residue 50 ILE Chi-restraints excluded: chain n residue 83 MET Chi-restraints excluded: chain n residue 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 199 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 353 optimal weight: 50.0000 chunk 290 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 292 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 415 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.141453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.103536 restraints weight = 125094.300| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 6.61 r_work: 0.3115 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 35725 Z= 0.233 Angle : 0.661 9.942 48765 Z= 0.329 Chirality : 0.046 0.307 5718 Planarity : 0.004 0.077 6146 Dihedral : 6.540 56.969 6326 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 1.51 % Allowed : 12.12 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % 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: 0.03 (0.13), residues: 4309 helix: 1.77 (0.19), residues: 695 sheet: 0.56 (0.14), residues: 1354 loop : -0.89 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG j 87 TYR 0.028 0.002 TYR B 423 PHE 0.029 0.002 PHE B 486 TRP 0.045 0.002 TRP i 99 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00544 (35595) covalent geometry : angle 0.63859 (48428) SS BOND : bond 0.00337 ( 53) SS BOND : angle 1.33516 ( 106) hydrogen bonds : bond 0.04183 ( 1376) hydrogen bonds : angle 5.39989 ( 3861) link_BETA1-4 : bond 0.00506 ( 31) link_BETA1-4 : angle 2.26063 ( 93) link_NAG-ASN : bond 0.00546 ( 46) link_NAG-ASN : angle 2.53581 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 116 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: j 19 ARG cc_start: 0.6370 (ttm-80) cc_final: 0.6168 (ttm-80) REVERT: j 54 ASP cc_start: 0.7533 (p0) cc_final: 0.7280 (p0) REVERT: A 206 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7754 (tmtt) REVERT: A 237 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7147 (ttp80) REVERT: A 619 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: A 1050 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.7849 (ptp) REVERT: B 449 TYR cc_start: 0.7702 (m-80) cc_final: 0.7471 (m-80) REVERT: B 584 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7591 (pt) REVERT: B 784 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: C 858 LEU cc_start: 0.9102 (tt) cc_final: 0.8467 (mp) REVERT: g 84 ASP cc_start: 0.3222 (m-30) cc_final: 0.2801 (m-30) REVERT: g 85 GLU cc_start: 0.4879 (tm-30) cc_final: 0.4478 (mt-10) REVERT: g 99 TRP cc_start: 0.5648 (m-90) cc_final: 0.5312 (m-90) REVERT: g 143 PHE cc_start: 0.2841 (p90) cc_final: 0.2599 (p90) REVERT: n 185 LEU cc_start: 0.1940 (OUTLIER) cc_final: 0.1407 (tt) outliers start: 57 outliers final: 42 residues processed: 163 average time/residue: 0.2136 time to fit residues: 59.1963 Evaluate side-chains 161 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1118 HIS Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1118 HIS Chi-restraints excluded: chain g residue 18 ILE Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 90 CYS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 48 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain l residue 50 ILE Chi-restraints excluded: chain n residue 83 MET Chi-restraints excluded: chain n residue 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 336 optimal weight: 0.9990 chunk 394 optimal weight: 0.7980 chunk 401 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 365 optimal weight: 30.0000 chunk 237 optimal weight: 0.6980 chunk 430 optimal weight: 10.0000 chunk 234 optimal weight: 0.7980 chunk 1 optimal weight: 0.0060 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 31 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.143675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.106666 restraints weight = 125064.479| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 7.79 r_work: 0.3206 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35725 Z= 0.109 Angle : 0.589 12.720 48765 Z= 0.294 Chirality : 0.044 0.292 5718 Planarity : 0.004 0.076 6146 Dihedral : 6.227 56.387 6326 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 1.35 % Allowed : 12.31 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.79 % 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: 0.14 (0.13), residues: 4309 helix: 2.01 (0.20), residues: 692 sheet: 0.57 (0.14), residues: 1351 loop : -0.82 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG j 87 TYR 0.025 0.001 TYR g 51 PHE 0.027 0.001 PHE C 342 TRP 0.053 0.002 TRP l 37 HIS 0.003 0.001 HIS i 202 Details of bonding type rmsd covalent geometry : bond 0.00232 (35595) covalent geometry : angle 0.57005 (48428) SS BOND : bond 0.00220 ( 53) SS BOND : angle 1.05339 ( 106) hydrogen bonds : bond 0.03475 ( 1376) hydrogen bonds : angle 5.15076 ( 3861) link_BETA1-4 : bond 0.00643 ( 31) link_BETA1-4 : angle 2.11426 ( 93) link_NAG-ASN : bond 0.00356 ( 46) link_NAG-ASN : angle 2.17478 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15315.82 seconds wall clock time: 260 minutes 48.19 seconds (15648.19 seconds total)