Starting phenix.real_space_refine on Sun Jul 5 13:30:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zrv_14922/07_2026/7zrv_14922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrv_14922/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zrv_14922/07_2026/7zrv_14922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrv_14922/07_2026/7zrv_14922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zrv_14922/07_2026/7zrv_14922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrv_14922/07_2026/7zrv_14922.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zrv_14922/07_2026/7zrv_14922.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zrv_14922/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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 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 chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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 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 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 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 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 chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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 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 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 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 chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 4 Time building chain proxies: 6.00, 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: 2.39 Conformation dependent library (CDL) restraints added in 990.4 milliseconds 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: 0.97 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: 6.54 Time building geometry restraints manager: 2.97 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 - 18.00: 14915 18.00 - 36.00: 1253 36.00 - 53.99: 198 53.99 - 71.99: 47 71.99 - 89.99: 23 Dihedral angle restraints: 16436 sinusoidal: 6450 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 16433 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.260 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 13.447 89.988 9892 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/Z covalent geometry : bond 0.00364 / 0.18 (28692) covalent geometry : angle 0.62521 / 0.29 (39015) SS BOND : bond 0.00224 / 0.16 ( 42) SS BOND : angle 0.96580 / 0.56 ( 84) hydrogen bonds : bond 0.18530 / 12.36 ( 960) hydrogen bonds : angle 7.67160 / 5.25 ( 2751) Misc. bond : bond 0.00081 / 0.04 ( 1) link_BETA1-4 : bond 0.00715 / 0.49 ( 42) link_BETA1-4 : angle 1.99577 / 1.39 ( 126) link_NAG-ASN : bond 0.00455 / 0.32 ( 46) link_NAG-ASN : angle 2.62673 / 1.82 ( 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 : 0.794 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: 0.4272 time to fit residues: 128.7370 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 : 0.677 ------------------------------------------------------------------------------- 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... 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 = 0.134807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.082293 restraints weight = 61134.528| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.72 r_work: 0.3178 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1399 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= 0.225 Angle : 0.688 11.392 39363 Z= 0.334 Chirality : 0.049 0.351 4638 Planarity : 0.004 0.051 4933 Dihedral : 4.120 27.397 3700 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.80 % Favored : 93.99 % Rotamer: Outliers : 1.14 % Allowed : 7.94 % Favored : 90.92 % 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: 1.89 (0.19), residues: 784 sheet: -0.24 (0.21), residues: 606 loop : -1.10 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 31 TYR 0.034 0.002 TYR C 837 PHE 0.033 0.002 PHE B 166 TRP 0.020 0.002 TRP C 436 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (28692) covalent geometry : angle 0.66299 / 0.33 (39015) SS BOND : bond 0.00339 / 0.22 ( 42) SS BOND : angle 1.18769 / 0.70 ( 84) hydrogen bonds : bond 0.04672 / 3.09 ( 960) hydrogen bonds : angle 5.86790 / 3.97 ( 2751) Misc. bond : bond 0.00045 / 0.02 ( 1) link_BETA1-4 : bond 0.00693 / 0.46 ( 42) link_BETA1-4 : angle 1.95393 / 1.36 ( 126) link_NAG-ASN : bond 0.00471 / 0.33 ( 46) link_NAG-ASN : angle 2.49938 / 1.77 ( 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 : 0.827 Fit side-chains revert: symmetry clash REVERT: A 100 ASN cc_start: 0.7026 (OUTLIER) cc_final: 0.6634 (p0) REVERT: A 151 MET cc_start: 0.2566 (tmm) cc_final: 0.2338 (ptp) REVERT: A 421 TYR cc_start: 0.6849 (m-10) cc_final: 0.6540 (m-80) REVERT: A 422 ASN cc_start: 0.7374 (m110) cc_final: 0.6951 (m-40) REVERT: B 67 TRP cc_start: 0.8313 (t60) cc_final: 0.7803 (t60) REVERT: B 565 PHE cc_start: 0.6575 (m-10) cc_final: 0.6366 (m-10) REVERT: B 751 ASN cc_start: 0.9200 (m110) cc_final: 0.8894 (m110) REVERT: B 855 PHE cc_start: 0.8244 (t80) cc_final: 0.7946 (t80) REVERT: C 33 ASN cc_start: 0.8811 (t0) cc_final: 0.8323 (t0) REVERT: C 357 ARG cc_start: 0.6514 (ttt-90) cc_final: 0.6147 (tmm-80) REVERT: C 759 PHE cc_start: 0.8414 (t80) cc_final: 0.8074 (t80) REVERT: F 39 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8546 (tm-30) outliers start: 34 outliers final: 15 residues processed: 194 average time/residue: 0.3869 time to fit residues: 95.5803 Evaluate side-chains 162 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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: 0.7980 chunk 106 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 252 optimal weight: 20.0000 chunk 293 optimal weight: 3.9990 chunk 264 optimal weight: 20.0000 chunk 168 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.135391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.084672 restraints weight = 59766.803| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.67 r_work: 0.3190 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28823 Z= 0.146 Angle : 0.634 11.708 39363 Z= 0.302 Chirality : 0.047 0.407 4638 Planarity : 0.004 0.048 4933 Dihedral : 3.957 17.804 3695 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.00 % Favored : 94.82 % Rotamer: Outliers : 1.21 % Allowed : 10.70 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3397 helix: 1.86 (0.19), residues: 793 sheet: -0.29 (0.21), residues: 610 loop : -1.10 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.022 0.001 TYR C 837 PHE 0.028 0.001 PHE B 166 TRP 0.015 0.001 TRP B 105 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (28692) covalent geometry : angle 0.60442 / 0.30 (39015) SS BOND : bond 0.00251 / 0.16 ( 42) SS BOND : angle 1.10850 / 0.63 ( 84) hydrogen bonds : bond 0.04163 / 2.75 ( 960) hydrogen bonds : angle 5.52533 / 3.74 ( 2751) Misc. bond : bond 0.00265 / 0.14 ( 1) link_BETA1-4 : bond 0.00677 / 0.47 ( 42) link_BETA1-4 : angle 1.90021 / 1.31 ( 126) link_NAG-ASN : bond 0.00615 / 0.36 ( 46) link_NAG-ASN : angle 2.69644 / 1.93 ( 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 201 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8211 (m) cc_final: 0.7842 (p) REVERT: A 96 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8114 (pp) REVERT: A 151 MET cc_start: 0.2611 (tmm) cc_final: 0.2396 (ptp) REVERT: A 175 MET cc_start: 0.7977 (mmt) cc_final: 0.7691 (pmm) REVERT: A 421 TYR cc_start: 0.7004 (m-80) cc_final: 0.6795 (m-80) REVERT: A 918 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8804 (pm20) REVERT: B 67 TRP cc_start: 0.8646 (t60) cc_final: 0.8270 (t60) REVERT: B 362 VAL cc_start: 0.6437 (OUTLIER) cc_final: 0.6218 (m) REVERT: B 751 ASN cc_start: 0.9227 (m110) cc_final: 0.8927 (m110) REVERT: B 855 PHE cc_start: 0.8180 (t80) cc_final: 0.7796 (t80) REVERT: C 33 ASN cc_start: 0.8852 (t0) cc_final: 0.8330 (t0) REVERT: C 357 ARG cc_start: 0.6793 (ttt-90) cc_final: 0.6439 (tmm-80) REVERT: F 39 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8545 (tm-30) outliers start: 36 outliers final: 17 residues processed: 186 average time/residue: 0.3943 time to fit residues: 91.7294 Evaluate side-chains 159 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER 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 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 994 ASP 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 582 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 991 VAL 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: 5.9990 chunk 164 optimal weight: 10.0000 chunk 276 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 184 optimal weight: 0.0570 chunk 127 optimal weight: 0.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.134563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.084126 restraints weight = 59086.123| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.61 r_work: 0.3177 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28823 Z= 0.160 Angle : 0.630 10.597 39363 Z= 0.301 Chirality : 0.047 0.396 4638 Planarity : 0.004 0.046 4933 Dihedral : 3.968 18.814 3695 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 2.15 % Allowed : 11.64 % Favored : 86.20 % 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: -0.35 (0.14), residues: 3397 helix: 1.85 (0.19), residues: 795 sheet: -0.29 (0.21), residues: 638 loop : -1.13 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 457 TYR 0.021 0.001 TYR C 837 PHE 0.026 0.001 PHE B 166 TRP 0.018 0.001 TRP B 105 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (28692) covalent geometry : angle 0.60306 / 0.29 (39015) SS BOND : bond 0.00254 / 0.16 ( 42) SS BOND : angle 1.11576 / 0.64 ( 84) hydrogen bonds : bond 0.03988 / 2.63 ( 960) hydrogen bonds : angle 5.33970 / 3.61 ( 2751) Misc. bond : bond 0.00776 / 0.41 ( 1) link_BETA1-4 : bond 0.00654 / 0.45 ( 42) link_BETA1-4 : angle 1.82936 / 1.27 ( 126) link_NAG-ASN : bond 0.00523 / 0.34 ( 46) link_NAG-ASN : angle 2.55685 / 1.81 ( 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 230 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.7966 (p) REVERT: A 175 MET cc_start: 0.7975 (mmt) cc_final: 0.7434 (mpp) REVERT: A 421 TYR cc_start: 0.6940 (m-10) cc_final: 0.6628 (m-10) REVERT: A 422 ASN cc_start: 0.7374 (m110) cc_final: 0.6912 (m-40) REVERT: A 918 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8812 (pm20) REVERT: B 67 TRP cc_start: 0.8856 (t60) cc_final: 0.8479 (t-100) REVERT: B 362 VAL cc_start: 0.6370 (OUTLIER) cc_final: 0.6134 (m) REVERT: B 751 ASN cc_start: 0.9278 (m110) cc_final: 0.8943 (m110) REVERT: B 756 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.6261 (t80) REVERT: B 855 PHE cc_start: 0.8235 (t80) cc_final: 0.7828 (t80) REVERT: C 33 ASN cc_start: 0.8826 (t0) cc_final: 0.8297 (t0) REVERT: C 151 MET cc_start: 0.4184 (tpt) cc_final: 0.3817 (tmt) REVERT: C 740 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8166 (ppp) REVERT: F 39 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8507 (tm-30) outliers start: 64 outliers final: 27 residues processed: 208 average time/residue: 0.3999 time to fit residues: 105.8281 Evaluate side-chains 179 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 B residue 1094 VAL 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 267 VAL Chi-restraints excluded: chain C residue 546 LEU 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: 2.9990 chunk 192 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 255 optimal weight: 20.0000 chunk 28 optimal weight: 0.0570 chunk 291 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 246 optimal weight: 0.0030 overall best weight: 0.9712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 135 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN 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 = 0.135433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.084778 restraints weight = 59301.643| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.66 r_work: 0.3189 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28823 Z= 0.125 Angle : 0.624 12.071 39363 Z= 0.295 Chirality : 0.047 0.409 4638 Planarity : 0.004 0.097 4933 Dihedral : 3.924 17.996 3695 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.36 % Favored : 94.47 % Rotamer: Outliers : 2.15 % Allowed : 13.19 % Favored : 84.66 % 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: 1.91 (0.19), residues: 795 sheet: -0.26 (0.21), residues: 629 loop : -1.13 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 403 TYR 0.025 0.001 TYR C 837 PHE 0.022 0.001 PHE A 515 TRP 0.023 0.001 TRP B 105 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (28692) covalent geometry : angle 0.59890 / 0.29 (39015) SS BOND : bond 0.00231 / 0.15 ( 42) SS BOND : angle 1.05018 / 0.59 ( 84) hydrogen bonds : bond 0.03747 / 2.49 ( 960) hydrogen bonds : angle 5.18441 / 3.51 ( 2751) Misc. bond : bond 0.00096 / 0.05 ( 1) link_BETA1-4 : bond 0.00658 / 0.46 ( 42) link_BETA1-4 : angle 1.77313 / 1.24 ( 126) link_NAG-ASN : bond 0.00503 / 0.33 ( 46) link_NAG-ASN : angle 2.50502 / 1.78 ( 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 231 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 167 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7875 (mmt) cc_final: 0.7331 (pmm) REVERT: A 421 TYR cc_start: 0.6923 (m-80) cc_final: 0.6716 (m-10) REVERT: A 918 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8825 (pm20) REVERT: A 1138 TYR cc_start: 0.8707 (t80) cc_final: 0.8374 (t80) REVERT: B 67 TRP cc_start: 0.8803 (t60) cc_final: 0.8452 (t-100) REVERT: B 126 ASN cc_start: 0.8238 (m-40) cc_final: 0.7890 (t0) REVERT: B 354 ASN cc_start: 0.9108 (t0) cc_final: 0.8270 (p0) REVERT: B 362 VAL cc_start: 0.6350 (OUTLIER) cc_final: 0.6121 (m) REVERT: B 751 ASN cc_start: 0.9272 (m110) cc_final: 0.8950 (m110) REVERT: B 756 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.6026 (t80) REVERT: B 855 PHE cc_start: 0.8242 (t80) cc_final: 0.7829 (t80) REVERT: C 33 ASN cc_start: 0.8855 (t0) cc_final: 0.8276 (t0) REVERT: C 135 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7678 (pp30) REVERT: C 151 MET cc_start: 0.4031 (tpt) cc_final: 0.3749 (tmt) REVERT: C 357 ARG cc_start: 0.6754 (ttt-90) cc_final: 0.6468 (tmm-80) REVERT: C 740 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8132 (ppp) REVERT: C 752 LEU cc_start: 0.9093 (pp) cc_final: 0.8799 (mt) REVERT: F 35 ARG cc_start: 0.7991 (mmp80) cc_final: 0.7752 (mmt-90) outliers start: 64 outliers final: 24 residues processed: 212 average time/residue: 0.4019 time to fit residues: 107.8314 Evaluate side-chains 181 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 433 VAL 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 106 ILE Chi-restraints excluded: chain B residue 242 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 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 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: 5.9990 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 170 optimal weight: 0.0010 chunk 63 optimal weight: 5.9990 chunk 76 optimal weight: 0.0980 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN E 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.134674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.083997 restraints weight = 59176.982| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.66 r_work: 0.3176 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28823 Z= 0.150 Angle : 0.631 10.703 39363 Z= 0.299 Chirality : 0.047 0.389 4638 Planarity : 0.004 0.062 4933 Dihedral : 3.918 18.828 3695 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.41 % Rotamer: Outliers : 2.25 % Allowed : 13.93 % Favored : 83.82 % 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: 1.89 (0.19), residues: 796 sheet: -0.26 (0.21), residues: 647 loop : -1.12 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 20 TYR 0.023 0.001 TYR C 837 PHE 0.023 0.001 PHE A 93 TRP 0.024 0.001 TRP B 105 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (28692) covalent geometry : angle 0.60576 / 0.29 (39015) SS BOND : bond 0.00248 / 0.16 ( 42) SS BOND : angle 1.05766 / 0.61 ( 84) hydrogen bonds : bond 0.03782 / 2.51 ( 960) hydrogen bonds : angle 5.14718 / 3.49 ( 2751) Misc. bond : bond 0.00372 / 0.20 ( 1) link_BETA1-4 : bond 0.00642 / 0.44 ( 42) link_BETA1-4 : angle 1.77587 / 1.24 ( 126) link_NAG-ASN : bond 0.00480 / 0.31 ( 46) link_NAG-ASN : angle 2.48532 / 1.77 ( 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 226 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 159 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7855 (mmt) cc_final: 0.7396 (mpp) REVERT: A 270 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 408 ARG cc_start: 0.8510 (mmp80) cc_final: 0.8192 (tpp-160) REVERT: A 421 TYR cc_start: 0.7030 (m-80) cc_final: 0.6806 (m-10) REVERT: A 918 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8943 (pm20) REVERT: A 1138 TYR cc_start: 0.8684 (t80) cc_final: 0.8482 (t80) REVERT: B 67 TRP cc_start: 0.8824 (t60) cc_final: 0.8483 (t-100) REVERT: B 354 ASN cc_start: 0.9103 (t0) cc_final: 0.8259 (p0) REVERT: B 362 VAL cc_start: 0.6383 (OUTLIER) cc_final: 0.6145 (m) REVERT: B 619 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: B 751 ASN cc_start: 0.9301 (m110) cc_final: 0.8962 (m110) REVERT: B 756 TYR cc_start: 0.6458 (OUTLIER) cc_final: 0.6138 (t80) REVERT: B 855 PHE cc_start: 0.8239 (t80) cc_final: 0.7834 (t80) REVERT: C 33 ASN cc_start: 0.8857 (t0) cc_final: 0.8273 (t0) REVERT: C 151 MET cc_start: 0.4008 (tpt) cc_final: 0.3706 (tmt) REVERT: C 740 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8188 (ppp) outliers start: 67 outliers final: 33 residues processed: 205 average time/residue: 0.4138 time to fit residues: 109.2763 Evaluate side-chains 191 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 270 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL 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 242 LEU Chi-restraints excluded: chain B residue 277 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 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL 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 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 574 ASP 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: 6.9990 chunk 28 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 271 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 218 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.133827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.082920 restraints weight = 59427.719| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.66 r_work: 0.3149 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28823 Z= 0.183 Angle : 0.654 10.447 39363 Z= 0.311 Chirality : 0.048 0.438 4638 Planarity : 0.004 0.055 4933 Dihedral : 4.037 18.851 3695 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 2.59 % Allowed : 14.37 % Favored : 83.04 % 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: -0.35 (0.15), residues: 3397 helix: 1.81 (0.19), residues: 796 sheet: -0.26 (0.21), residues: 641 loop : -1.13 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 20 TYR 0.021 0.001 TYR C1067 PHE 0.031 0.001 PHE B 490 TRP 0.029 0.002 TRP B 105 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (28692) covalent geometry : angle 0.62901 / 0.31 (39015) SS BOND : bond 0.00278 / 0.18 ( 42) SS BOND : angle 1.13629 / 0.66 ( 84) hydrogen bonds : bond 0.03972 / 2.63 ( 960) hydrogen bonds : angle 5.19214 / 3.53 ( 2751) Misc. bond : bond 0.00286 / 0.15 ( 1) link_BETA1-4 : bond 0.00647 / 0.45 ( 42) link_BETA1-4 : angle 1.81671 / 1.27 ( 126) link_NAG-ASN : bond 0.00489 / 0.33 ( 46) link_NAG-ASN : angle 2.52297 / 1.79 ( 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 240 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 163 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.7849 (mmt) cc_final: 0.7330 (ptp) REVERT: A 242 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8338 (mm) REVERT: A 270 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8260 (mp) REVERT: A 342 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: A 408 ARG cc_start: 0.8539 (mmp80) cc_final: 0.8298 (tpp-160) REVERT: A 421 TYR cc_start: 0.7054 (m-80) cc_final: 0.6827 (m-10) REVERT: A 918 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8894 (pm20) REVERT: A 1138 TYR cc_start: 0.8747 (t80) cc_final: 0.8476 (t80) REVERT: B 67 TRP cc_start: 0.8891 (t60) cc_final: 0.8531 (t-100) REVERT: B 106 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8300 (tp) REVERT: B 362 VAL cc_start: 0.6335 (OUTLIER) cc_final: 0.6080 (m) REVERT: B 619 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: B 751 ASN cc_start: 0.9305 (m110) cc_final: 0.8968 (m110) REVERT: B 855 PHE cc_start: 0.8254 (t80) cc_final: 0.7843 (t80) REVERT: C 33 ASN cc_start: 0.8755 (t0) cc_final: 0.8153 (t0) REVERT: C 106 ILE cc_start: 0.8488 (pp) cc_final: 0.8255 (pp) REVERT: C 241 LEU cc_start: 0.8448 (mm) cc_final: 0.7516 (tp) REVERT: C 740 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8223 (ppp) REVERT: F 35 ARG cc_start: 0.8044 (mmp80) cc_final: 0.7827 (mmt-90) REVERT: F 39 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8383 (pp30) outliers start: 77 outliers final: 40 residues processed: 212 average time/residue: 0.4273 time to fit residues: 116.0893 Evaluate side-chains 193 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU 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 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 697 MET 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 106 ILE 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 994 ASP Chi-restraints excluded: chain B residue 1094 VAL 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 574 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 206 optimal weight: 0.9980 chunk 256 optimal weight: 20.0000 chunk 285 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 213 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.132042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.082174 restraints weight = 59848.827| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.65 r_work: 0.3143 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2468 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= 0.194 Angle : 0.665 11.701 39363 Z= 0.316 Chirality : 0.048 0.403 4638 Planarity : 0.004 0.055 4933 Dihedral : 4.089 18.809 3695 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.65 % Favored : 94.17 % Rotamer: Outliers : 2.25 % Allowed : 15.04 % Favored : 82.71 % 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: -0.40 (0.14), residues: 3397 helix: 1.77 (0.19), residues: 796 sheet: -0.38 (0.21), residues: 637 loop : -1.11 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 20 TYR 0.021 0.001 TYR C 904 PHE 0.035 0.001 PHE B 166 TRP 0.033 0.002 TRP B 105 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (28692) covalent geometry : angle 0.64062 / 0.31 (39015) SS BOND : bond 0.00289 / 0.19 ( 42) SS BOND : angle 1.16977 / 0.69 ( 84) hydrogen bonds : bond 0.04019 / 2.65 ( 960) hydrogen bonds : angle 5.21530 / 3.54 ( 2751) Misc. bond : bond 0.00552 / 0.29 ( 1) link_BETA1-4 : bond 0.00654 / 0.45 ( 42) link_BETA1-4 : angle 1.83687 / 1.28 ( 126) link_NAG-ASN : bond 0.00492 / 0.33 ( 46) link_NAG-ASN : angle 2.51906 / 1.79 ( 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 219 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 152 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7817 (mmt) cc_final: 0.7312 (mpp) REVERT: A 342 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: A 421 TYR cc_start: 0.7162 (m-80) cc_final: 0.6912 (m-80) REVERT: A 756 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7891 (t80) REVERT: A 918 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8929 (pm20) REVERT: A 1138 TYR cc_start: 0.8785 (t80) cc_final: 0.8506 (t80) REVERT: B 67 TRP cc_start: 0.8945 (t60) cc_final: 0.8569 (t-100) REVERT: B 106 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8274 (tp) REVERT: B 362 VAL cc_start: 0.6400 (OUTLIER) cc_final: 0.6139 (m) REVERT: B 619 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: B 751 ASN cc_start: 0.9318 (m110) cc_final: 0.8968 (m110) REVERT: B 855 PHE cc_start: 0.8230 (t80) cc_final: 0.7827 (t80) REVERT: B 1029 MET cc_start: 0.9083 (tpp) cc_final: 0.8762 (tpp) REVERT: C 33 ASN cc_start: 0.8751 (t0) cc_final: 0.8156 (t0) REVERT: C 357 ARG cc_start: 0.6487 (ttt-90) cc_final: 0.6150 (tmm-80) REVERT: C 740 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8245 (ppp) REVERT: F 39 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8434 (pp30) outliers start: 67 outliers final: 41 residues processed: 199 average time/residue: 0.4072 time to fit residues: 103.5109 Evaluate side-chains 192 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 66 THR 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 317 ASN 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 756 TYR 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 106 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 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 1094 VAL Chi-restraints excluded: chain B residue 1118 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 225 optimal weight: 20.0000 chunk 286 optimal weight: 0.6980 chunk 256 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 252 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 332 optimal weight: 20.0000 chunk 192 optimal weight: 0.9990 chunk 317 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 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 = 0.4146 r_free = 0.4146 target = 0.134255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.083583 restraints weight = 59681.607| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.66 r_work: 0.3167 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28823 Z= 0.141 Angle : 0.643 11.792 39363 Z= 0.305 Chirality : 0.047 0.396 4638 Planarity : 0.004 0.043 4933 Dihedral : 4.018 17.960 3695 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.36 % Favored : 94.47 % Rotamer: Outliers : 1.85 % Allowed : 15.48 % Favored : 82.67 % 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: -0.36 (0.15), residues: 3397 helix: 1.84 (0.19), residues: 802 sheet: -0.36 (0.21), residues: 646 loop : -1.12 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 634 TYR 0.020 0.001 TYR C1067 PHE 0.026 0.001 PHE C 377 TRP 0.042 0.002 TRP B 105 HIS 0.017 0.001 HIS F 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (28692) covalent geometry : angle 0.61895 / 0.30 (39015) SS BOND : bond 0.00246 / 0.16 ( 42) SS BOND : angle 1.10684 / 0.64 ( 84) hydrogen bonds : bond 0.03759 / 2.49 ( 960) hydrogen bonds : angle 5.10142 / 3.47 ( 2751) Misc. bond : bond 0.00461 / 0.24 ( 1) link_BETA1-4 : bond 0.00653 / 0.45 ( 42) link_BETA1-4 : angle 1.79101 / 1.24 ( 126) link_NAG-ASN : bond 0.00491 / 0.32 ( 46) link_NAG-ASN : angle 2.45524 / 1.75 ( 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 215 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7880 (mmt) cc_final: 0.7246 (ptp) REVERT: A 242 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8411 (mm) REVERT: A 421 TYR cc_start: 0.7089 (m-80) cc_final: 0.6836 (m-80) REVERT: A 756 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7806 (t80) REVERT: A 918 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8919 (pm20) REVERT: A 1138 TYR cc_start: 0.8764 (t80) cc_final: 0.8464 (t80) REVERT: B 67 TRP cc_start: 0.8954 (t60) cc_final: 0.8546 (t-100) REVERT: B 106 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8253 (tp) REVERT: B 362 VAL cc_start: 0.6349 (OUTLIER) cc_final: 0.6105 (m) REVERT: B 619 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: B 751 ASN cc_start: 0.9312 (m110) cc_final: 0.8961 (m110) REVERT: B 855 PHE cc_start: 0.8230 (t80) cc_final: 0.7825 (t80) REVERT: B 1029 MET cc_start: 0.8936 (tpp) cc_final: 0.8601 (tpp) REVERT: C 33 ASN cc_start: 0.8804 (t0) cc_final: 0.8194 (t0) REVERT: C 106 ILE cc_start: 0.8523 (pp) cc_final: 0.8283 (pp) REVERT: C 193 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7956 (ttpt) REVERT: C 241 LEU cc_start: 0.8349 (mm) cc_final: 0.7492 (tp) REVERT: C 357 ARG cc_start: 0.6573 (ttt-90) cc_final: 0.6241 (tmm-80) REVERT: C 740 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8198 (ppp) REVERT: F 8 GLN cc_start: 0.7495 (pp30) cc_final: 0.7128 (mm110) REVERT: F 20 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.7773 (mmm160) REVERT: F 39 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8442 (pp30) outliers start: 55 outliers final: 37 residues processed: 197 average time/residue: 0.3959 time to fit residues: 98.5209 Evaluate side-chains 190 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 317 ASN 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 756 TYR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 973 ILE 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 106 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 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 666 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1094 VAL 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 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 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 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: 0.6980 chunk 183 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 257 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 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 = 0.4136 r_free = 0.4136 target = 0.132718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.083219 restraints weight = 59472.702| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.62 r_work: 0.3164 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28823 Z= 0.154 Angle : 0.655 11.961 39363 Z= 0.310 Chirality : 0.048 0.421 4638 Planarity : 0.004 0.043 4933 Dihedral : 4.020 19.092 3695 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 1.78 % Allowed : 15.68 % 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: -0.37 (0.15), residues: 3397 helix: 1.83 (0.19), residues: 799 sheet: -0.37 (0.21), residues: 644 loop : -1.12 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 634 TYR 0.022 0.001 TYR C 904 PHE 0.041 0.001 PHE B 166 TRP 0.047 0.002 TRP B 105 HIS 0.021 0.001 HIS F 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (28692) covalent geometry : angle 0.63139 / 0.30 (39015) SS BOND : bond 0.00245 / 0.16 ( 42) SS BOND : angle 1.11702 / 0.64 ( 84) hydrogen bonds : bond 0.03787 / 2.51 ( 960) hydrogen bonds : angle 5.07996 / 3.46 ( 2751) Misc. bond : bond 0.00462 / 0.24 ( 1) link_BETA1-4 : bond 0.00658 / 0.45 ( 42) link_BETA1-4 : angle 1.78615 / 1.24 ( 126) link_NAG-ASN : bond 0.00486 / 0.32 ( 46) link_NAG-ASN : angle 2.46943 / 1.76 ( 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 206 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7879 (mmt) cc_final: 0.7248 (ptp) REVERT: A 242 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8405 (mm) REVERT: A 342 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: A 421 TYR cc_start: 0.7133 (m-80) cc_final: 0.6872 (m-80) REVERT: A 756 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7813 (t80) REVERT: A 902 MET cc_start: 0.9129 (tpp) cc_final: 0.8922 (mmm) REVERT: A 918 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8753 (pm20) REVERT: A 1138 TYR cc_start: 0.8655 (t80) cc_final: 0.8345 (t80) REVERT: B 67 TRP cc_start: 0.8885 (t60) cc_final: 0.8486 (t-100) REVERT: B 106 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8283 (tp) REVERT: B 362 VAL cc_start: 0.6392 (OUTLIER) cc_final: 0.6135 (m) REVERT: B 402 ILE cc_start: 0.8481 (pt) cc_final: 0.8269 (pt) REVERT: B 619 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: B 751 ASN cc_start: 0.9312 (m110) cc_final: 0.8961 (m110) REVERT: B 855 PHE cc_start: 0.8237 (t80) cc_final: 0.7842 (t80) REVERT: C 33 ASN cc_start: 0.8808 (t0) cc_final: 0.8205 (t0) REVERT: C 193 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7952 (ttpt) REVERT: C 357 ARG cc_start: 0.6623 (ttt-90) cc_final: 0.6297 (tmm-80) REVERT: C 740 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8232 (ppp) REVERT: F 39 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8387 (pp30) outliers start: 53 outliers final: 40 residues processed: 190 average time/residue: 0.4112 time to fit residues: 99.7080 Evaluate side-chains 194 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 317 ASN 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 641 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 973 ILE 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 106 ILE 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 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 B residue 1094 VAL 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 267 VAL Chi-restraints excluded: chain C residue 483 VAL 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 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 162 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 333 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 170 optimal weight: 0.0980 chunk 161 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.132262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.082615 restraints weight = 59444.811| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.62 r_work: 0.3160 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28823 Z= 0.171 Angle : 0.664 12.243 39363 Z= 0.315 Chirality : 0.048 0.414 4638 Planarity : 0.004 0.043 4933 Dihedral : 4.067 18.083 3695 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.48 % Favored : 94.35 % Rotamer: Outliers : 1.72 % Allowed : 15.88 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3397 helix: 1.78 (0.19), residues: 801 sheet: -0.36 (0.21), residues: 623 loop : -1.16 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 31 TYR 0.024 0.001 TYR C 904 PHE 0.026 0.001 PHE C 377 TRP 0.045 0.002 TRP B 105 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (28692) covalent geometry : angle 0.64011 / 0.31 (39015) SS BOND : bond 0.00264 / 0.18 ( 42) SS BOND : angle 1.13519 / 0.67 ( 84) hydrogen bonds : bond 0.03863 / 2.56 ( 960) hydrogen bonds : angle 5.11467 / 3.48 ( 2751) Misc. bond : bond 0.00314 / 0.17 ( 1) link_BETA1-4 : bond 0.00657 / 0.45 ( 42) link_BETA1-4 : angle 1.81137 / 1.26 ( 126) link_NAG-ASN : bond 0.00483 / 0.32 ( 46) link_NAG-ASN : angle 2.47983 / 1.76 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9934.07 seconds wall clock time: 170 minutes 0.15 seconds (10200.15 seconds total)