Starting phenix.real_space_refine on Fri Mar 6 04:40:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrv_14922/03_2026/7zrv_14922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrv_14922/03_2026/7zrv_14922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zrv_14922/03_2026/7zrv_14922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrv_14922/03_2026/7zrv_14922.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrv_14922/03_2026/7zrv_14922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrv_14922/03_2026/7zrv_14922.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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 119 5.16 5 C 17846 2.51 5 N 4582 2.21 5 O 5508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28055 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8623 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8589 Classifications: {'peptide': 1096} Link IDs: {'PTRANS': 56, 'TRANS': 1039} Chain breaks: 4 Chain: "C" Number of atoms: 8609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8609 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1043} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "F" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 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: "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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.80, per 1000 atoms: 0.21 Number of scatterers: 28055 At special positions: 0 Unit cell: (146.87, 151.807, 209.814, 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 119 16.00 O 5508 8.00 N 4582 7.00 C 17846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 164 " 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=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 164 " 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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 B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 164 " 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 C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 64 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 64 " " NAG C1301 " - " ASN C 603 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 234 " " NAG D 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 282 " " NAG N 1 " - " ASN A 162 " " NAG O 1 " - " ASN A 123 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN B 709 " " NAG V 1 " - " ASN B 343 " " NAG W 1 " - " ASN B 282 " " NAG X 1 " - " ASN B 123 " " NAG Y 1 " - " ASN B 162 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C1134 " " NAG e 1 " - " ASN C 709 " " NAG f 1 " - " ASN C 331 " " NAG g 1 " - " ASN C 343 " " NAG h 1 " - " ASN C 126 " " NAG i 1 " - " ASN C 162 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.3 seconds 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6418 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 49 sheets defined 25.7% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.509A pdb=" N ASN A 75 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 158 removed outlier: 4.412A pdb=" N PHE A 155 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 157 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 158 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.961A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.763A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 756 Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.117A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 849 through 855 removed outlier: 3.549A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.780A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.314A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 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: 4.602A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.556A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.976A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.776A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 Processing helix chain 'B' and resid 828 through 830 No H-bonds generated for 'chain 'B' and resid 828 through 830' Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 940 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: 3.525A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.658A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.866A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.832A pdb=" N LEU C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 759 through 782 removed outlier: 3.528A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 827 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.897A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.552A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.448A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 26 through 49 Processing helix chain 'F' and resid 3 through 25 Processing helix chain 'F' and resid 26 through 49 removed outlier: 3.677A pdb=" N ALA F 30 " --> pdb=" O ASN F 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 3.676A pdb=" N VAL A 267 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 7.055A pdb=" N VAL A 39 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 227 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 58 removed outlier: 3.563A pdb=" N GLN A 271 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 102 through 103 removed outlier: 3.644A pdb=" N ARG A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.547A pdb=" N PHE A 166 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU A 133 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N CYS A 164 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.792A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.549A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.747A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.857A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.805A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 5.734A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.223A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 33 Processing sheet with id=AC1, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 58 removed outlier: 3.600A pdb=" N VAL B 50 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 58 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.507A pdb=" N TYR B 202 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 193 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 227 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.830A pdb=" N ARG B 237 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY B 108 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.421A pdb=" N PHE B 166 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 135 through 136 removed outlier: 6.551A pdb=" N GLN B 135 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 313 through 319 removed outlier: 7.169A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.721A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.576A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.988A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.522A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.522A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.668A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 31 through 33 Processing sheet with id=AD9, first strand: chain 'C' and resid 52 through 58 removed outlier: 3.930A pdb=" N ASP C 56 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AE2, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.583A pdb=" N TYR C 202 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 193 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 227 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.598A pdb=" N GLY C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 116 through 117 removed outlier: 7.573A pdb=" N VAL C 131 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 165 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.694A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.875A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.580A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.511A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.511A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.359A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.316A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2751 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: 5.86 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8813 1.34 - 1.46: 6628 1.46 - 1.58: 13100 1.58 - 1.70: 0 1.70 - 1.82: 151 Bond restraints: 28692 Sorted by residual: bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.54e+00 ... (remaining 28687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 37698 1.53 - 3.07: 1056 3.07 - 4.60: 169 4.60 - 6.13: 76 6.13 - 7.67: 16 Bond angle restraints: 39015 Sorted by residual: angle pdb=" N ILE A 101 " pdb=" CA ILE A 101 " pdb=" C ILE A 101 " ideal model delta sigma weight residual 113.71 108.58 5.13 9.50e-01 1.11e+00 2.92e+01 angle pdb=" C LYS B 854 " pdb=" CA LYS B 854 " pdb=" CB LYS B 854 " ideal model delta sigma weight residual 115.79 110.71 5.08 1.19e+00 7.06e-01 1.82e+01 angle pdb=" C GLY C 594 " pdb=" N VAL C 595 " pdb=" CA VAL C 595 " ideal model delta sigma weight residual 121.97 127.65 -5.68 1.80e+00 3.09e-01 9.96e+00 angle pdb=" N GLN B 774 " pdb=" CA GLN B 774 " pdb=" CB GLN B 774 " ideal model delta sigma weight residual 110.28 115.00 -4.72 1.55e+00 4.16e-01 9.29e+00 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.11e+00 ... (remaining 39010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 16973 24.09 - 48.18: 906 48.18 - 72.27: 164 72.27 - 96.36: 104 96.36 - 120.45: 113 Dihedral angle restraints: 18260 sinusoidal: 8274 harmonic: 9986 Sorted by residual: dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual 93.00 177.95 -84.95 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -159.99 73.99 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 166.75 -73.75 1 1.00e+01 1.00e-02 6.91e+01 ... (remaining 18257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4419 0.102 - 0.204: 194 0.204 - 0.305: 21 0.305 - 0.407: 2 0.407 - 0.509: 2 Chirality restraints: 4638 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.47e+00 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C 126 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN C 162 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 4635 not shown) Planarity restraints: 4979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 599 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.30e+00 pdb=" N PRO C 600 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 600 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 600 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 67 " -0.014 2.00e-02 2.50e+03 1.42e-02 5.06e+00 pdb=" CG TRP C 67 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 67 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 67 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 67 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 67 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 67 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 67 " -0.012 2.00e-02 2.50e+03 1.39e-02 4.80e+00 pdb=" CG TRP B 67 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 67 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 67 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 67 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 67 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 67 " 0.000 2.00e-02 2.50e+03 ... (remaining 4976 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 444 2.65 - 3.21: 26633 3.21 - 3.78: 43456 3.78 - 4.34: 58711 4.34 - 4.90: 95760 Nonbonded interactions: 225004 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR B 904 " pdb=" O GLY C1093 " model vdw 2.099 3.040 nonbonded pdb=" OG1 THR B 110 " pdb=" OD1 ASP B 112 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.185 3.040 nonbonded pdb=" O PHE B 486 " pdb=" NE2 GLN F 9 " model vdw 2.208 3.120 ... (remaining 224999 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 22 through 840 or resid 851 through 1304)) selection = (chain 'B' and resid 22 through 1304) selection = (chain 'C' and (resid 22 through 840 or resid 851 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 25.500 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.004 0.078 28823 Z= 0.180 Angle : 0.653 10.844 39363 Z= 0.301 Chirality : 0.049 0.509 4638 Planarity : 0.003 0.058 4933 Dihedral : 18.634 120.451 11716 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3397 helix: 1.87 (0.19), residues: 809 sheet: -0.03 (0.22), residues: 616 loop : -1.05 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 357 TYR 0.022 0.001 TYR B 904 PHE 0.029 0.001 PHE C 184 TRP 0.039 0.002 TRP C 67 HIS 0.013 0.001 HIS F 15 Details of bonding type rmsd covalent geometry : bond 0.00364 (28692) covalent geometry : angle 0.62521 (39015) SS BOND : bond 0.00224 ( 42) SS BOND : angle 0.96580 ( 84) hydrogen bonds : bond 0.18530 ( 960) hydrogen bonds : angle 7.67160 ( 2751) Misc. bond : bond 0.00081 ( 1) link_BETA1-4 : bond 0.00715 ( 42) link_BETA1-4 : angle 1.99577 ( 126) link_NAG-ASN : bond 0.00455 ( 46) link_NAG-ASN : angle 2.62673 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.1815 (tmm) cc_final: 0.0673 (ptp) REVERT: A 396 TYR cc_start: 0.6788 (m-10) cc_final: 0.6587 (m-10) REVERT: B 266 TYR cc_start: 0.8033 (m-80) cc_final: 0.7828 (m-80) REVERT: B 400 PHE cc_start: 0.8274 (p90) cc_final: 0.8053 (p90) REVERT: B 751 ASN cc_start: 0.8896 (m110) cc_final: 0.8674 (m110) REVERT: C 33 ASN cc_start: 0.8454 (t0) cc_final: 0.8182 (t0) REVERT: C 322 PRO cc_start: 0.6728 (Cg_exo) cc_final: 0.6387 (Cg_endo) REVERT: C 357 ARG cc_start: 0.6413 (ttt-90) cc_final: 0.6157 (tmm-80) REVERT: C 740 MET cc_start: 0.7844 (ppp) cc_final: 0.7609 (ppp) REVERT: F 39 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8649 (tm-30) outliers start: 0 outliers final: 2 residues processed: 236 average time/residue: 0.4541 time to fit residues: 132.5705 Evaluate side-chains 151 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 1092 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 100 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN ** F 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.134773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.082201 restraints weight = 61125.448| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.70 r_work: 0.3176 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28823 Z= 0.231 Angle : 0.739 11.408 39363 Z= 0.348 Chirality : 0.051 0.375 4638 Planarity : 0.004 0.051 4933 Dihedral : 15.124 108.206 5524 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.77 % Favored : 94.02 % Rotamer: Outliers : 1.14 % Allowed : 7.97 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3397 helix: 1.89 (0.19), residues: 784 sheet: -0.25 (0.21), residues: 606 loop : -1.10 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 31 TYR 0.035 0.002 TYR C 837 PHE 0.034 0.002 PHE B 166 TRP 0.021 0.002 TRP C 436 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00531 (28692) covalent geometry : angle 0.70839 (39015) SS BOND : bond 0.00347 ( 42) SS BOND : angle 1.21421 ( 84) hydrogen bonds : bond 0.04579 ( 960) hydrogen bonds : angle 5.84999 ( 2751) Misc. bond : bond 0.00474 ( 1) link_BETA1-4 : bond 0.00779 ( 42) link_BETA1-4 : angle 2.63628 ( 126) link_NAG-ASN : bond 0.00489 ( 46) link_NAG-ASN : angle 2.59788 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 100 ASN cc_start: 0.7033 (OUTLIER) cc_final: 0.6633 (p0) REVERT: A 151 MET cc_start: 0.2566 (tmm) cc_final: 0.2332 (ptp) REVERT: B 67 TRP cc_start: 0.8457 (t60) cc_final: 0.7976 (t60) REVERT: B 565 PHE cc_start: 0.6583 (m-10) cc_final: 0.6375 (m-10) REVERT: B 751 ASN cc_start: 0.9200 (m110) cc_final: 0.8893 (m110) REVERT: B 855 PHE cc_start: 0.8231 (t80) cc_final: 0.7916 (t80) REVERT: C 33 ASN cc_start: 0.8810 (t0) cc_final: 0.8317 (t0) REVERT: C 357 ARG cc_start: 0.6525 (ttt-90) cc_final: 0.6155 (tmm-80) REVERT: C 759 PHE cc_start: 0.8406 (t80) cc_final: 0.8059 (t80) REVERT: F 39 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8546 (tm-30) outliers start: 34 outliers final: 15 residues processed: 194 average time/residue: 0.4123 time to fit residues: 101.3488 Evaluate side-chains 159 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 339 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 60 optimal weight: 0.0370 chunk 160 optimal weight: 2.9990 chunk 252 optimal weight: 20.0000 chunk 293 optimal weight: 3.9990 chunk 264 optimal weight: 20.0000 chunk 168 optimal weight: 0.5980 chunk 300 optimal weight: 2.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN B1002 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C1142 GLN E 9 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.136764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.086176 restraints weight = 59561.706| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.69 r_work: 0.3221 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28823 Z= 0.119 Angle : 0.661 13.011 39363 Z= 0.304 Chirality : 0.048 0.404 4638 Planarity : 0.004 0.048 4933 Dihedral : 12.385 109.571 5519 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.92 % Favored : 94.91 % Rotamer: Outliers : 1.38 % Allowed : 10.30 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3397 helix: 1.99 (0.19), residues: 786 sheet: -0.27 (0.21), residues: 609 loop : -1.10 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 31 TYR 0.022 0.001 TYR C 837 PHE 0.028 0.001 PHE B 166 TRP 0.017 0.001 TRP B 105 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00254 (28692) covalent geometry : angle 0.62993 (39015) SS BOND : bond 0.00225 ( 42) SS BOND : angle 1.06734 ( 84) hydrogen bonds : bond 0.03990 ( 960) hydrogen bonds : angle 5.40189 ( 2751) Misc. bond : bond 0.00093 ( 1) link_BETA1-4 : bond 0.00728 ( 42) link_BETA1-4 : angle 2.45165 ( 126) link_NAG-ASN : bond 0.00513 ( 46) link_NAG-ASN : angle 2.48067 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7811 (p) REVERT: A 96 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.8011 (pp) REVERT: A 151 MET cc_start: 0.2459 (tmm) cc_final: 0.2124 (ptp) REVERT: A 175 MET cc_start: 0.8028 (mmt) cc_final: 0.7537 (pmm) REVERT: A 421 TYR cc_start: 0.6621 (m-80) cc_final: 0.5759 (m-80) REVERT: A 422 ASN cc_start: 0.7364 (m110) cc_final: 0.6852 (m-40) REVERT: A 918 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8792 (pm20) REVERT: A 950 ASP cc_start: 0.8511 (t0) cc_final: 0.8263 (t0) REVERT: B 67 TRP cc_start: 0.8648 (t60) cc_final: 0.8285 (t60) REVERT: B 354 ASN cc_start: 0.9098 (t0) cc_final: 0.8308 (p0) REVERT: B 751 ASN cc_start: 0.9266 (m110) cc_final: 0.8957 (m110) REVERT: B 855 PHE cc_start: 0.8176 (t80) cc_final: 0.7789 (t80) REVERT: C 33 ASN cc_start: 0.8863 (t0) cc_final: 0.8315 (t0) REVERT: C 241 LEU cc_start: 0.8516 (mm) cc_final: 0.7668 (tp) REVERT: C 357 ARG cc_start: 0.6793 (ttt-90) cc_final: 0.6440 (tmm-80) REVERT: F 29 LYS cc_start: 0.7446 (tppt) cc_final: 0.7241 (tppt) REVERT: F 39 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8539 (tm-30) outliers start: 41 outliers final: 17 residues processed: 203 average time/residue: 0.4755 time to fit residues: 119.0728 Evaluate side-chains 170 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 222 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 276 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 184 optimal weight: 0.0670 chunk 127 optimal weight: 0.9980 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.134967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.083923 restraints weight = 59425.990| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.68 r_work: 0.3176 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28823 Z= 0.163 Angle : 0.660 10.622 39363 Z= 0.308 Chirality : 0.047 0.433 4638 Planarity : 0.004 0.045 4933 Dihedral : 10.816 108.668 5519 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.48 % Favored : 94.35 % Rotamer: Outliers : 1.99 % Allowed : 12.21 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3397 helix: 1.97 (0.19), residues: 788 sheet: -0.26 (0.21), residues: 638 loop : -1.13 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.020 0.001 TYR C1067 PHE 0.023 0.001 PHE A 93 TRP 0.019 0.001 TRP B 105 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00374 (28692) covalent geometry : angle 0.62747 (39015) SS BOND : bond 0.00259 ( 42) SS BOND : angle 1.10532 ( 84) hydrogen bonds : bond 0.03939 ( 960) hydrogen bonds : angle 5.28175 ( 2751) Misc. bond : bond 0.00958 ( 1) link_BETA1-4 : bond 0.00706 ( 42) link_BETA1-4 : angle 2.51605 ( 126) link_NAG-ASN : bond 0.00444 ( 46) link_NAG-ASN : angle 2.54055 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 164 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7756 (p) REVERT: A 175 MET cc_start: 0.7984 (mmt) cc_final: 0.7514 (mpp) REVERT: A 242 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8254 (mm) REVERT: A 421 TYR cc_start: 0.6749 (m-80) cc_final: 0.6091 (m-80) REVERT: A 918 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8809 (pm20) REVERT: A 950 ASP cc_start: 0.8577 (t0) cc_final: 0.8351 (t0) REVERT: B 67 TRP cc_start: 0.8850 (t60) cc_final: 0.8473 (t-100) REVERT: B 354 ASN cc_start: 0.9109 (t0) cc_final: 0.8274 (p0) REVERT: B 362 VAL cc_start: 0.6322 (OUTLIER) cc_final: 0.6065 (m) REVERT: B 751 ASN cc_start: 0.9269 (m110) cc_final: 0.8947 (m110) REVERT: B 756 TYR cc_start: 0.6367 (OUTLIER) cc_final: 0.6043 (t80) REVERT: B 855 PHE cc_start: 0.8236 (t80) cc_final: 0.7822 (t80) REVERT: C 33 ASN cc_start: 0.8825 (t0) cc_final: 0.8291 (t0) REVERT: C 151 MET cc_start: 0.3723 (tpt) cc_final: 0.3450 (tmt) REVERT: C 740 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8218 (ppp) outliers start: 59 outliers final: 23 residues processed: 204 average time/residue: 0.4054 time to fit residues: 104.9581 Evaluate side-chains 180 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 88 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 193 optimal weight: 0.5980 chunk 255 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 0.0170 chunk 246 optimal weight: 0.0770 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 135 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.137027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.086341 restraints weight = 59200.034| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.70 r_work: 0.3226 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28823 Z= 0.110 Angle : 0.638 12.594 39363 Z= 0.295 Chirality : 0.047 0.427 4638 Planarity : 0.004 0.102 4933 Dihedral : 10.092 107.821 5519 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 1.82 % Allowed : 13.63 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3397 helix: 1.98 (0.19), residues: 797 sheet: -0.21 (0.21), residues: 632 loop : -1.11 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.026 0.001 TYR C 837 PHE 0.019 0.001 PHE A 515 TRP 0.023 0.001 TRP B 105 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00233 (28692) covalent geometry : angle 0.60592 (39015) SS BOND : bond 0.00201 ( 42) SS BOND : angle 1.00299 ( 84) hydrogen bonds : bond 0.03545 ( 960) hydrogen bonds : angle 5.08142 ( 2751) Misc. bond : bond 0.00469 ( 1) link_BETA1-4 : bond 0.00712 ( 42) link_BETA1-4 : angle 2.43645 ( 126) link_NAG-ASN : bond 0.00485 ( 46) link_NAG-ASN : angle 2.47292 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8490 (t80) cc_final: 0.8227 (t80) REVERT: A 175 MET cc_start: 0.7843 (mmt) cc_final: 0.7373 (pmm) REVERT: A 421 TYR cc_start: 0.6856 (m-80) cc_final: 0.6252 (m-80) REVERT: A 918 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8795 (pm20) REVERT: A 1138 TYR cc_start: 0.8715 (t80) cc_final: 0.8415 (t80) REVERT: B 67 TRP cc_start: 0.8802 (t60) cc_final: 0.8477 (t-100) REVERT: B 354 ASN cc_start: 0.9094 (t0) cc_final: 0.8267 (p0) REVERT: B 362 VAL cc_start: 0.6334 (OUTLIER) cc_final: 0.6105 (m) REVERT: B 490 PHE cc_start: 0.6092 (t80) cc_final: 0.5864 (t80) REVERT: B 751 ASN cc_start: 0.9289 (m110) cc_final: 0.8950 (m110) REVERT: B 756 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.5834 (t80) REVERT: B 855 PHE cc_start: 0.8217 (t80) cc_final: 0.7820 (t80) REVERT: C 33 ASN cc_start: 0.8847 (t0) cc_final: 0.8237 (t0) REVERT: C 106 ILE cc_start: 0.8498 (pp) cc_final: 0.8223 (pp) REVERT: C 135 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7675 (pp30) REVERT: C 151 MET cc_start: 0.4019 (tpt) cc_final: 0.3732 (tmt) REVERT: C 241 LEU cc_start: 0.8413 (mm) cc_final: 0.7624 (tp) REVERT: C 357 ARG cc_start: 0.6389 (tmm160) cc_final: 0.6102 (tmm-80) REVERT: C 740 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8064 (ppp) REVERT: C 752 LEU cc_start: 0.8995 (pp) cc_final: 0.8780 (mt) REVERT: F 29 LYS cc_start: 0.7530 (tppt) cc_final: 0.7326 (tppp) outliers start: 54 outliers final: 23 residues processed: 206 average time/residue: 0.4383 time to fit residues: 112.9109 Evaluate side-chains 186 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain E residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 230 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 255 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN B 82 ASN B 218 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.133494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082192 restraints weight = 59538.161| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.68 r_work: 0.3150 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28823 Z= 0.217 Angle : 0.691 10.349 39363 Z= 0.325 Chirality : 0.048 0.425 4638 Planarity : 0.004 0.060 4933 Dihedral : 9.626 108.228 5519 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 2.39 % Allowed : 13.93 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.15), residues: 3397 helix: 1.82 (0.19), residues: 804 sheet: -0.29 (0.21), residues: 634 loop : -1.11 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 20 TYR 0.025 0.002 TYR C 837 PHE 0.023 0.002 PHE A 93 TRP 0.026 0.002 TRP B 105 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00505 (28692) covalent geometry : angle 0.65857 (39015) SS BOND : bond 0.00304 ( 42) SS BOND : angle 1.16561 ( 84) hydrogen bonds : bond 0.04151 ( 960) hydrogen bonds : angle 5.21914 ( 2751) Misc. bond : bond 0.00538 ( 1) link_BETA1-4 : bond 0.00677 ( 42) link_BETA1-4 : angle 2.60166 ( 126) link_NAG-ASN : bond 0.00467 ( 46) link_NAG-ASN : angle 2.57527 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 162 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7246 (mp) REVERT: A 175 MET cc_start: 0.7883 (mmt) cc_final: 0.7408 (mpp) REVERT: A 270 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8305 (mp) REVERT: A 342 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: A 408 ARG cc_start: 0.8545 (mmp80) cc_final: 0.8246 (tpp-160) REVERT: A 421 TYR cc_start: 0.6858 (m-80) cc_final: 0.6204 (m-80) REVERT: A 918 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8842 (pm20) REVERT: B 67 TRP cc_start: 0.8863 (t60) cc_final: 0.8502 (t-100) REVERT: B 619 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: B 751 ASN cc_start: 0.9307 (m110) cc_final: 0.8968 (m110) REVERT: B 855 PHE cc_start: 0.8253 (t80) cc_final: 0.7842 (t80) REVERT: C 33 ASN cc_start: 0.8752 (t0) cc_final: 0.8162 (t0) REVERT: C 151 MET cc_start: 0.4016 (tpt) cc_final: 0.3691 (tmt) REVERT: C 740 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8349 (ppp) outliers start: 71 outliers final: 34 residues processed: 210 average time/residue: 0.4009 time to fit residues: 107.4221 Evaluate side-chains 183 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 255 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1002 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.134349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083531 restraints weight = 59397.941| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.66 r_work: 0.3168 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28823 Z= 0.152 Angle : 0.660 11.788 39363 Z= 0.308 Chirality : 0.047 0.450 4638 Planarity : 0.004 0.057 4933 Dihedral : 9.146 109.252 5519 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.41 % Rotamer: Outliers : 2.05 % Allowed : 14.84 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 3397 helix: 1.90 (0.19), residues: 798 sheet: -0.26 (0.21), residues: 635 loop : -1.13 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 20 TYR 0.022 0.001 TYR C 837 PHE 0.019 0.001 PHE B 456 TRP 0.031 0.001 TRP B 105 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00348 (28692) covalent geometry : angle 0.62719 (39015) SS BOND : bond 0.00253 ( 42) SS BOND : angle 1.09764 ( 84) hydrogen bonds : bond 0.03804 ( 960) hydrogen bonds : angle 5.11669 ( 2751) Misc. bond : bond 0.00131 ( 1) link_BETA1-4 : bond 0.00682 ( 42) link_BETA1-4 : angle 2.52121 ( 126) link_NAG-ASN : bond 0.00478 ( 46) link_NAG-ASN : angle 2.55370 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 161 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6502 (t80) REVERT: A 175 MET cc_start: 0.7835 (mmt) cc_final: 0.7330 (ptp) REVERT: A 342 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: A 408 ARG cc_start: 0.8541 (mmp80) cc_final: 0.8319 (tpp-160) REVERT: A 421 TYR cc_start: 0.7118 (m-80) cc_final: 0.6521 (m-80) REVERT: A 918 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8883 (pm20) REVERT: B 67 TRP cc_start: 0.8890 (t60) cc_final: 0.8539 (t-100) REVERT: B 354 ASN cc_start: 0.9078 (t0) cc_final: 0.8209 (p0) REVERT: B 362 VAL cc_start: 0.6368 (OUTLIER) cc_final: 0.6119 (m) REVERT: B 619 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: B 751 ASN cc_start: 0.9307 (m110) cc_final: 0.8968 (m110) REVERT: B 855 PHE cc_start: 0.8216 (t80) cc_final: 0.7814 (t80) REVERT: C 33 ASN cc_start: 0.8754 (t0) cc_final: 0.8136 (t0) REVERT: C 357 ARG cc_start: 0.6230 (tmm160) cc_final: 0.5952 (tmm-80) REVERT: C 740 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8228 (ppp) REVERT: F 39 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8102 (mm110) outliers start: 61 outliers final: 34 residues processed: 202 average time/residue: 0.4153 time to fit residues: 106.5869 Evaluate side-chains 188 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 206 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 285 optimal weight: 0.0070 chunk 308 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN E 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.133398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082396 restraints weight = 59759.114| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.64 r_work: 0.3140 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 28823 Z= 0.198 Angle : 0.687 11.574 39363 Z= 0.321 Chirality : 0.048 0.436 4638 Planarity : 0.004 0.051 4933 Dihedral : 8.794 108.832 5519 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.74 % Favored : 94.08 % Rotamer: Outliers : 2.09 % Allowed : 14.97 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 3397 helix: 1.84 (0.19), residues: 796 sheet: -0.30 (0.21), residues: 625 loop : -1.16 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 32 TYR 0.021 0.001 TYR C1067 PHE 0.036 0.001 PHE B 166 TRP 0.037 0.002 TRP B 105 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00458 (28692) covalent geometry : angle 0.65356 (39015) SS BOND : bond 0.00291 ( 42) SS BOND : angle 1.16497 ( 84) hydrogen bonds : bond 0.04032 ( 960) hydrogen bonds : angle 5.17817 ( 2751) Misc. bond : bond 0.00846 ( 1) link_BETA1-4 : bond 0.00677 ( 42) link_BETA1-4 : angle 2.58176 ( 126) link_NAG-ASN : bond 0.00455 ( 46) link_NAG-ASN : angle 2.60651 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 150 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7712 (t80) cc_final: 0.6976 (t80) REVERT: A 101 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7293 (mp) REVERT: A 175 MET cc_start: 0.7841 (mmt) cc_final: 0.7349 (mpp) REVERT: A 242 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8394 (mm) REVERT: A 270 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 342 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: A 421 TYR cc_start: 0.6997 (m-80) cc_final: 0.6359 (m-80) REVERT: A 918 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8752 (pm20) REVERT: B 67 TRP cc_start: 0.8942 (t60) cc_final: 0.8554 (t-100) REVERT: B 362 VAL cc_start: 0.6387 (OUTLIER) cc_final: 0.6120 (m) REVERT: B 619 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: B 751 ASN cc_start: 0.9318 (m110) cc_final: 0.8958 (m110) REVERT: B 855 PHE cc_start: 0.8210 (t80) cc_final: 0.7806 (t80) REVERT: B 1050 MET cc_start: 0.9195 (ptm) cc_final: 0.8981 (ptp) REVERT: C 33 ASN cc_start: 0.8753 (t0) cc_final: 0.8148 (t0) REVERT: C 357 ARG cc_start: 0.6190 (tmm160) cc_final: 0.5893 (tmm-80) REVERT: C 740 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8308 (ppp) REVERT: F 39 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8124 (mm110) outliers start: 62 outliers final: 42 residues processed: 190 average time/residue: 0.4152 time to fit residues: 99.9770 Evaluate side-chains 196 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 225 optimal weight: 9.9990 chunk 286 optimal weight: 0.6980 chunk 256 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 306 optimal weight: 0.8980 chunk 252 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 332 optimal weight: 20.0000 chunk 192 optimal weight: 0.5980 chunk 317 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN E 9 GLN F 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.133032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.083452 restraints weight = 59550.415| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.64 r_work: 0.3178 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28823 Z= 0.142 Angle : 0.664 11.833 39363 Z= 0.309 Chirality : 0.047 0.428 4638 Planarity : 0.004 0.049 4933 Dihedral : 8.493 108.169 5519 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.45 % Favored : 94.38 % Rotamer: Outliers : 1.99 % Allowed : 15.44 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.15), residues: 3397 helix: 1.90 (0.19), residues: 800 sheet: -0.32 (0.21), residues: 637 loop : -1.15 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 634 TYR 0.020 0.001 TYR C1067 PHE 0.022 0.001 PHE A 93 TRP 0.044 0.002 TRP B 105 HIS 0.017 0.001 HIS F 15 Details of bonding type rmsd covalent geometry : bond 0.00323 (28692) covalent geometry : angle 0.63160 (39015) SS BOND : bond 0.00245 ( 42) SS BOND : angle 1.08548 ( 84) hydrogen bonds : bond 0.03779 ( 960) hydrogen bonds : angle 5.08691 ( 2751) Misc. bond : bond 0.00118 ( 1) link_BETA1-4 : bond 0.00651 ( 42) link_BETA1-4 : angle 2.52215 ( 126) link_NAG-ASN : bond 0.00446 ( 46) link_NAG-ASN : angle 2.57161 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7877 (mmt) cc_final: 0.7289 (ptp) REVERT: A 421 TYR cc_start: 0.7117 (m-80) cc_final: 0.6492 (m-80) REVERT: A 918 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8725 (pm20) REVERT: A 1141 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9126 (tt) REVERT: B 67 TRP cc_start: 0.8962 (t60) cc_final: 0.8565 (t-100) REVERT: B 354 ASN cc_start: 0.9087 (t0) cc_final: 0.8201 (p0) REVERT: B 362 VAL cc_start: 0.6425 (OUTLIER) cc_final: 0.6173 (m) REVERT: B 619 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: B 751 ASN cc_start: 0.9320 (m110) cc_final: 0.8967 (m110) REVERT: B 855 PHE cc_start: 0.8209 (t80) cc_final: 0.7795 (t80) REVERT: C 33 ASN cc_start: 0.8758 (t0) cc_final: 0.8130 (t0) REVERT: C 106 ILE cc_start: 0.8544 (pp) cc_final: 0.8310 (pp) REVERT: C 193 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7972 (ttpt) REVERT: C 241 LEU cc_start: 0.8353 (mm) cc_final: 0.7492 (tp) REVERT: C 357 ARG cc_start: 0.6192 (tmm160) cc_final: 0.5886 (tmm-80) REVERT: C 740 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8276 (ppp) REVERT: F 8 GLN cc_start: 0.7491 (pp30) cc_final: 0.7175 (mm110) REVERT: F 39 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8122 (mm110) outliers start: 59 outliers final: 39 residues processed: 197 average time/residue: 0.4413 time to fit residues: 108.7071 Evaluate side-chains 194 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 171 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 164 optimal weight: 0.0270 chunk 34 optimal weight: 0.9980 chunk 208 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 chunk 305 optimal weight: 0.6980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.135531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.084917 restraints weight = 59421.505| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.68 r_work: 0.3204 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28823 Z= 0.115 Angle : 0.658 13.183 39363 Z= 0.305 Chirality : 0.047 0.435 4638 Planarity : 0.004 0.043 4933 Dihedral : 8.084 105.035 5519 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.21 % Favored : 94.61 % Rotamer: Outliers : 1.55 % Allowed : 15.92 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 3397 helix: 1.94 (0.19), residues: 803 sheet: -0.33 (0.21), residues: 639 loop : -1.13 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 35 TYR 0.020 0.001 TYR C1067 PHE 0.040 0.001 PHE B 166 TRP 0.051 0.002 TRP B 105 HIS 0.017 0.001 HIS F 15 Details of bonding type rmsd covalent geometry : bond 0.00252 (28692) covalent geometry : angle 0.62715 (39015) SS BOND : bond 0.00198 ( 42) SS BOND : angle 1.01567 ( 84) hydrogen bonds : bond 0.03528 ( 960) hydrogen bonds : angle 4.94852 ( 2751) Misc. bond : bond 0.00619 ( 1) link_BETA1-4 : bond 0.00624 ( 42) link_BETA1-4 : angle 2.42313 ( 126) link_NAG-ASN : bond 0.00460 ( 46) link_NAG-ASN : angle 2.52981 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7846 (mmt) cc_final: 0.7273 (ptp) REVERT: A 421 TYR cc_start: 0.7123 (m-80) cc_final: 0.6504 (m-80) REVERT: A 918 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8645 (pm20) REVERT: B 67 TRP cc_start: 0.8859 (t60) cc_final: 0.8445 (t-100) REVERT: B 354 ASN cc_start: 0.9079 (t0) cc_final: 0.8210 (p0) REVERT: B 362 VAL cc_start: 0.6415 (OUTLIER) cc_final: 0.6172 (m) REVERT: B 402 ILE cc_start: 0.8465 (pt) cc_final: 0.8245 (pt) REVERT: B 619 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: B 751 ASN cc_start: 0.9320 (m110) cc_final: 0.8961 (m110) REVERT: B 855 PHE cc_start: 0.8239 (t80) cc_final: 0.7828 (t80) REVERT: C 33 ASN cc_start: 0.8806 (t0) cc_final: 0.8168 (t0) REVERT: C 106 ILE cc_start: 0.8529 (pp) cc_final: 0.8297 (pp) REVERT: C 193 LYS cc_start: 0.8333 (ttpt) cc_final: 0.8012 (ttpt) REVERT: C 241 LEU cc_start: 0.8283 (mm) cc_final: 0.7417 (tp) REVERT: C 357 ARG cc_start: 0.6202 (tmm160) cc_final: 0.5893 (tmm-80) REVERT: C 740 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8176 (ppp) REVERT: C 752 LEU cc_start: 0.9089 (pp) cc_final: 0.8827 (mt) REVERT: F 8 GLN cc_start: 0.7487 (pp30) cc_final: 0.7137 (mm110) REVERT: F 31 ARG cc_start: 0.8033 (mpt-90) cc_final: 0.7823 (mmm-85) REVERT: F 35 ARG cc_start: 0.7847 (mmp80) cc_final: 0.7427 (mmt180) REVERT: F 39 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8154 (mm110) outliers start: 46 outliers final: 35 residues processed: 197 average time/residue: 0.4461 time to fit residues: 110.0941 Evaluate side-chains 194 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 162 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 333 optimal weight: 9.9990 chunk 129 optimal weight: 0.3980 chunk 173 optimal weight: 3.9990 chunk 259 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 170 optimal weight: 0.0770 chunk 161 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.134179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.084982 restraints weight = 59442.226| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.63 r_work: 0.3203 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28823 Z= 0.121 Angle : 0.654 13.043 39363 Z= 0.304 Chirality : 0.047 0.440 4638 Planarity : 0.004 0.043 4933 Dihedral : 7.919 101.951 5519 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.27 % Favored : 94.55 % Rotamer: Outliers : 1.48 % Allowed : 16.22 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 3397 helix: 1.98 (0.19), residues: 797 sheet: -0.37 (0.20), residues: 650 loop : -1.13 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 408 TYR 0.022 0.001 TYR C 904 PHE 0.025 0.001 PHE A 166 TRP 0.049 0.002 TRP B 105 HIS 0.020 0.001 HIS F 15 Details of bonding type rmsd covalent geometry : bond 0.00271 (28692) covalent geometry : angle 0.62345 (39015) SS BOND : bond 0.00208 ( 42) SS BOND : angle 1.01037 ( 84) hydrogen bonds : bond 0.03530 ( 960) hydrogen bonds : angle 4.91910 ( 2751) Misc. bond : bond 0.00122 ( 1) link_BETA1-4 : bond 0.00634 ( 42) link_BETA1-4 : angle 2.39636 ( 126) link_NAG-ASN : bond 0.00443 ( 46) link_NAG-ASN : angle 2.50850 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10184.12 seconds wall clock time: 174 minutes 6.62 seconds (10446.62 seconds total)