Starting phenix.real_space_refine on Tue Jun 24 08:18:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrv_14922/06_2025/7zrv_14922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrv_14922/06_2025/7zrv_14922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zrv_14922/06_2025/7zrv_14922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrv_14922/06_2025/7zrv_14922.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrv_14922/06_2025/7zrv_14922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrv_14922/06_2025/7zrv_14922.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.43s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28055 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8623 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8589 Classifications: {'peptide': 1096} Link IDs: {'PTRANS': 56, 'TRANS': 1039} Chain breaks: 4 Chain: "C" Number of atoms: 8609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8609 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1043} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "F" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 15.20, per 1000 atoms: 0.54 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: 7.09 Conformation dependent library (CDL) restraints added in 3.0 seconds 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6418 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 49 sheets defined 25.7% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 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: 10.96 Time building geometry restraints manager: 8.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8813 1.34 - 1.46: 6628 1.46 - 1.58: 13100 1.58 - 1.70: 0 1.70 - 1.82: 151 Bond restraints: 28692 Sorted by residual: bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.54e+00 ... (remaining 28687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 37698 1.53 - 3.07: 1056 3.07 - 4.60: 169 4.60 - 6.13: 76 6.13 - 7.67: 16 Bond angle restraints: 39015 Sorted by residual: angle pdb=" N ILE A 101 " pdb=" CA ILE A 101 " pdb=" C ILE A 101 " ideal model delta sigma weight residual 113.71 108.58 5.13 9.50e-01 1.11e+00 2.92e+01 angle pdb=" C LYS B 854 " pdb=" CA LYS B 854 " pdb=" CB LYS B 854 " ideal model delta sigma weight residual 115.79 110.71 5.08 1.19e+00 7.06e-01 1.82e+01 angle pdb=" C GLY C 594 " pdb=" N VAL C 595 " pdb=" CA VAL C 595 " ideal model delta sigma weight residual 121.97 127.65 -5.68 1.80e+00 3.09e-01 9.96e+00 angle pdb=" N GLN B 774 " pdb=" CA GLN B 774 " pdb=" CB GLN B 774 " ideal model delta sigma weight residual 110.28 115.00 -4.72 1.55e+00 4.16e-01 9.29e+00 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.11e+00 ... (remaining 39010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 16973 24.09 - 48.18: 906 48.18 - 72.27: 164 72.27 - 96.36: 104 96.36 - 120.45: 113 Dihedral angle restraints: 18260 sinusoidal: 8274 harmonic: 9986 Sorted by residual: dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual 93.00 177.95 -84.95 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -159.99 73.99 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 166.75 -73.75 1 1.00e+01 1.00e-02 6.91e+01 ... (remaining 18257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4419 0.102 - 0.204: 194 0.204 - 0.305: 21 0.305 - 0.407: 2 0.407 - 0.509: 2 Chirality restraints: 4638 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.47e+00 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C 126 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN C 162 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 4635 not shown) Planarity restraints: 4979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 599 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.30e+00 pdb=" N PRO C 600 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 600 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 600 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 67 " -0.014 2.00e-02 2.50e+03 1.42e-02 5.06e+00 pdb=" CG TRP C 67 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 67 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 67 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 67 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 67 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 67 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 67 " -0.012 2.00e-02 2.50e+03 1.39e-02 4.80e+00 pdb=" CG TRP B 67 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 67 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 67 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 67 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 67 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 67 " 0.000 2.00e-02 2.50e+03 ... (remaining 4976 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 444 2.65 - 3.21: 26633 3.21 - 3.78: 43456 3.78 - 4.34: 58711 4.34 - 4.90: 95760 Nonbonded interactions: 225004 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR B 904 " pdb=" O GLY C1093 " model vdw 2.099 3.040 nonbonded pdb=" OG1 THR B 110 " pdb=" OD1 ASP B 112 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.185 3.040 nonbonded pdb=" O PHE B 486 " pdb=" NE2 GLN F 9 " model vdw 2.208 3.120 ... (remaining 224999 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 840 or resid 851 through 1147 or resid 1301 thr \ ough 1304)) selection = (chain 'B' and (resid 22 through 1147 or resid 1301 through 1304)) selection = (chain 'C' and (resid 22 through 840 or resid 851 through 1147 or resid 1301 thr \ ough 1304)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 59.330 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.190 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28823 Z= 0.180 Angle : 0.653 10.844 39363 Z= 0.301 Chirality : 0.049 0.509 4638 Planarity : 0.003 0.058 4933 Dihedral : 18.634 120.451 11716 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.039 0.002 TRP C 67 HIS 0.013 0.001 HIS F 15 PHE 0.029 0.001 PHE C 184 TYR 0.022 0.001 TYR B 904 ARG 0.007 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 46) link_NAG-ASN : angle 2.62673 ( 138) link_BETA1-4 : bond 0.00715 ( 42) link_BETA1-4 : angle 1.99577 ( 126) hydrogen bonds : bond 0.18530 ( 960) hydrogen bonds : angle 7.67160 ( 2751) SS BOND : bond 0.00224 ( 42) SS BOND : angle 0.96580 ( 84) covalent geometry : bond 0.00364 (28692) covalent geometry : angle 0.62521 (39015) Misc. bond : bond 0.00081 ( 1) *********************** 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 : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 VAL cc_start: 0.7955 (t) cc_final: 0.7752 (p) 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: 0.7829 (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: 0.8631 (tm-30) outliers start: 0 outliers final: 2 residues processed: 236 average time/residue: 0.9598 time to fit residues: 283.0688 Evaluate side-chains 152 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 3.227 ------------------------------------------------------------------------------- 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 287 optimal weight: 0.9980 chunk 258 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 174 optimal weight: 0.1980 chunk 138 optimal weight: 0.6980 chunk 267 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 309 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** F 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.138489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087163 restraints weight = 60444.532| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.70 r_work: 0.3268 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28823 Z= 0.128 Angle : 0.672 10.922 39363 Z= 0.314 Chirality : 0.048 0.376 4638 Planarity : 0.004 0.049 4933 Dihedral : 15.792 108.856 5524 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 0.84 % Allowed : 6.97 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3397 helix: 2.08 (0.19), residues: 779 sheet: -0.04 (0.21), residues: 624 loop : -1.07 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 PHE 0.031 0.001 PHE B 166 TYR 0.033 0.001 TYR C 837 ARG 0.006 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 46) link_NAG-ASN : angle 2.48139 ( 138) link_BETA1-4 : bond 0.00675 ( 42) link_BETA1-4 : angle 2.46300 ( 126) hydrogen bonds : bond 0.04242 ( 960) hydrogen bonds : angle 5.88309 ( 2751) SS BOND : bond 0.00241 ( 42) SS BOND : angle 0.98545 ( 84) covalent geometry : bond 0.00275 (28692) covalent geometry : angle 0.64157 (39015) Misc. bond : bond 0.00526 ( 1) *********************** 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 207 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 3.202 Fit side-chains revert: symmetry clash REVERT: A 100 ASN cc_start: 0.6664 (OUTLIER) cc_final: 0.6420 (p0) REVERT: A 151 MET cc_start: 0.2294 (tmm) cc_final: 0.1898 (ptp) REVERT: A 421 TYR cc_start: 0.6684 (m-10) cc_final: 0.6470 (m-80) REVERT: A 955 ASN cc_start: 0.7698 (m110) cc_final: 0.7494 (t0) REVERT: B 67 TRP cc_start: 0.8147 (t60) cc_final: 0.7934 (t60) REVERT: B 565 PHE cc_start: 0.6460 (m-10) cc_final: 0.6247 (m-10) REVERT: B 751 ASN cc_start: 0.9216 (m110) cc_final: 0.8927 (m110) REVERT: B 855 PHE cc_start: 0.8212 (t80) cc_final: 0.7883 (t80) REVERT: C 33 ASN cc_start: 0.8791 (t0) cc_final: 0.8280 (t0) REVERT: C 357 ARG cc_start: 0.6561 (ttt-90) cc_final: 0.6238 (tmm-80) REVERT: C 752 LEU cc_start: 0.8974 (pp) cc_final: 0.8660 (mt) REVERT: F 39 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8527 (tm-30) outliers start: 25 outliers final: 8 residues processed: 196 average time/residue: 0.9281 time to fit residues: 230.5923 Evaluate side-chains 155 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 387 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 582 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 44 optimal weight: 20.0000 chunk 183 optimal weight: 0.7980 chunk 281 optimal weight: 7.9990 chunk 197 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 265 optimal weight: 20.0000 chunk 249 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 218 optimal weight: 0.3980 chunk 238 optimal weight: 0.0050 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 774 GLN B1002 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.137834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.086569 restraints weight = 60321.502| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.65 r_work: 0.3257 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28823 Z= 0.129 Angle : 0.658 11.144 39363 Z= 0.303 Chirality : 0.048 0.401 4638 Planarity : 0.004 0.047 4933 Dihedral : 12.835 110.333 5519 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.97 % Favored : 94.82 % Rotamer: Outliers : 1.51 % Allowed : 9.12 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3397 helix: 2.02 (0.19), residues: 788 sheet: -0.13 (0.21), residues: 637 loop : -1.10 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 105 HIS 0.006 0.001 HIS B 519 PHE 0.026 0.001 PHE B 166 TYR 0.029 0.001 TYR C 837 ARG 0.005 0.000 ARG F 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 46) link_NAG-ASN : angle 2.66223 ( 138) link_BETA1-4 : bond 0.00696 ( 42) link_BETA1-4 : angle 2.45152 ( 126) hydrogen bonds : bond 0.03953 ( 960) hydrogen bonds : angle 5.44282 ( 2751) SS BOND : bond 0.00226 ( 42) SS BOND : angle 0.99170 ( 84) covalent geometry : bond 0.00284 (28692) covalent geometry : angle 0.62442 (39015) Misc. bond : bond 0.00500 ( 1) *********************** 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 218 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.2423 (tmm) cc_final: 0.2081 (ptp) REVERT: A 175 MET cc_start: 0.7954 (mmt) cc_final: 0.7529 (pmm) REVERT: A 421 TYR cc_start: 0.6767 (m-10) cc_final: 0.6397 (m-10) REVERT: A 422 ASN cc_start: 0.7392 (m110) cc_final: 0.6957 (m-40) REVERT: A 918 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8706 (pm20) REVERT: A 950 ASP cc_start: 0.8514 (t0) cc_final: 0.8260 (t0) REVERT: B 67 TRP cc_start: 0.8556 (t60) cc_final: 0.8262 (t60) REVERT: B 354 ASN cc_start: 0.9132 (t0) cc_final: 0.8387 (p0) REVERT: B 515 PHE cc_start: 0.7688 (m-10) cc_final: 0.7487 (m-10) REVERT: B 697 MET cc_start: 0.8774 (ptm) cc_final: 0.8375 (ptm) REVERT: B 751 ASN cc_start: 0.9187 (m110) cc_final: 0.8879 (m110) REVERT: B 855 PHE cc_start: 0.8229 (t80) cc_final: 0.7843 (t80) REVERT: C 33 ASN cc_start: 0.8851 (t0) cc_final: 0.8292 (t0) REVERT: C 241 LEU cc_start: 0.8453 (mm) cc_final: 0.7649 (tp) REVERT: C 752 LEU cc_start: 0.8927 (pp) cc_final: 0.8643 (mt) REVERT: C 759 PHE cc_start: 0.8546 (t80) cc_final: 0.8323 (t80) REVERT: F 39 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8525 (tm-30) outliers start: 45 outliers final: 16 residues processed: 200 average time/residue: 0.9350 time to fit residues: 236.8389 Evaluate side-chains 165 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 296 LEU 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 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 288 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 329 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.136603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.085757 restraints weight = 60061.529| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.70 r_work: 0.3217 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28823 Z= 0.139 Angle : 0.644 12.996 39363 Z= 0.298 Chirality : 0.047 0.425 4638 Planarity : 0.004 0.045 4933 Dihedral : 10.812 111.300 5519 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.30 % Favored : 94.52 % Rotamer: Outliers : 1.48 % Allowed : 11.31 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3397 helix: 1.97 (0.19), residues: 795 sheet: -0.19 (0.21), residues: 622 loop : -1.09 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 105 HIS 0.005 0.001 HIS B 519 PHE 0.027 0.001 PHE B 166 TYR 0.026 0.001 TYR C 837 ARG 0.011 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 46) link_NAG-ASN : angle 2.54170 ( 138) link_BETA1-4 : bond 0.00711 ( 42) link_BETA1-4 : angle 2.46136 ( 126) hydrogen bonds : bond 0.03764 ( 960) hydrogen bonds : angle 5.22711 ( 2751) SS BOND : bond 0.00246 ( 42) SS BOND : angle 1.08481 ( 84) covalent geometry : bond 0.00313 (28692) covalent geometry : angle 0.61103 (39015) Misc. bond : bond 0.00570 ( 1) *********************** 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 211 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 2.722 Fit side-chains revert: symmetry clash REVERT: A 151 MET cc_start: 0.2482 (tmm) cc_final: 0.2131 (ptp) REVERT: A 175 MET cc_start: 0.7894 (mmt) cc_final: 0.7405 (pmm) REVERT: A 342 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: A 421 TYR cc_start: 0.6945 (m-10) cc_final: 0.6690 (m-10) REVERT: A 918 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8782 (pm20) REVERT: A 950 ASP cc_start: 0.8610 (t0) cc_final: 0.8372 (t0) REVERT: A 1138 TYR cc_start: 0.8796 (t80) cc_final: 0.8582 (t80) REVERT: B 67 TRP cc_start: 0.8744 (t60) cc_final: 0.8443 (t-100) REVERT: B 354 ASN cc_start: 0.9105 (t0) cc_final: 0.8284 (p0) REVERT: B 362 VAL cc_start: 0.6418 (OUTLIER) cc_final: 0.6175 (m) REVERT: B 565 PHE cc_start: 0.6470 (m-10) cc_final: 0.6264 (m-10) REVERT: B 751 ASN cc_start: 0.9242 (m110) cc_final: 0.8924 (m110) REVERT: B 756 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.5965 (t80) REVERT: B 855 PHE cc_start: 0.8200 (t80) cc_final: 0.7829 (t80) REVERT: C 33 ASN cc_start: 0.8861 (t0) cc_final: 0.8314 (t0) REVERT: C 106 ILE cc_start: 0.8715 (pp) cc_final: 0.8471 (pp) REVERT: C 241 LEU cc_start: 0.8532 (mm) cc_final: 0.7689 (tp) outliers start: 44 outliers final: 20 residues processed: 197 average time/residue: 0.8689 time to fit residues: 218.7134 Evaluate side-chains 172 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 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 84 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 230 optimal weight: 7.9990 chunk 335 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.134693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083884 restraints weight = 59532.858| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.66 r_work: 0.3166 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28823 Z= 0.185 Angle : 0.666 10.590 39363 Z= 0.313 Chirality : 0.047 0.391 4638 Planarity : 0.004 0.044 4933 Dihedral : 10.045 107.786 5519 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.74 % Favored : 94.08 % Rotamer: Outliers : 1.85 % Allowed : 12.65 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3397 helix: 1.85 (0.19), residues: 803 sheet: -0.21 (0.21), residues: 649 loop : -1.13 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 105 HIS 0.005 0.001 HIS B 519 PHE 0.022 0.002 PHE A 93 TYR 0.030 0.002 TYR C 837 ARG 0.006 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 46) link_NAG-ASN : angle 2.56478 ( 138) link_BETA1-4 : bond 0.00730 ( 42) link_BETA1-4 : angle 2.50373 ( 126) hydrogen bonds : bond 0.04010 ( 960) hydrogen bonds : angle 5.22874 ( 2751) SS BOND : bond 0.00277 ( 42) SS BOND : angle 1.19805 ( 84) covalent geometry : bond 0.00429 (28692) covalent geometry : angle 0.63271 (39015) Misc. bond : bond 0.00588 ( 1) *********************** 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 215 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 3.035 Fit side-chains revert: symmetry clash REVERT: A 105 TRP cc_start: 0.8570 (m-90) cc_final: 0.8233 (m-90) REVERT: A 175 MET cc_start: 0.7940 (mmt) cc_final: 0.7235 (pmm) REVERT: A 342 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: A 408 ARG cc_start: 0.8229 (tpp-160) cc_final: 0.8013 (tpp-160) REVERT: A 421 TYR cc_start: 0.7127 (m-80) cc_final: 0.6529 (m-80) REVERT: A 918 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8810 (pm20) REVERT: B 67 TRP cc_start: 0.8760 (t60) cc_final: 0.8439 (t-100) REVERT: B 362 VAL cc_start: 0.6428 (OUTLIER) cc_final: 0.6184 (m) REVERT: B 565 PHE cc_start: 0.6563 (m-10) cc_final: 0.6354 (m-10) REVERT: B 751 ASN cc_start: 0.9293 (m110) cc_final: 0.8939 (m110) REVERT: B 855 PHE cc_start: 0.8270 (t80) cc_final: 0.7863 (t80) REVERT: C 33 ASN cc_start: 0.8802 (t0) cc_final: 0.8274 (t0) REVERT: C 357 ARG cc_start: 0.6395 (tmm160) cc_final: 0.6150 (tmm-80) REVERT: C 740 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8267 (ppp) outliers start: 55 outliers final: 27 residues processed: 197 average time/residue: 0.9070 time to fit residues: 228.6811 Evaluate side-chains 176 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER 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 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 993 ILE 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 296 LEU 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 756 TYR Chi-restraints excluded: chain B residue 994 ASP 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 203 SER Chi-restraints excluded: chain C residue 267 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 333 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 257 optimal weight: 20.0000 chunk 154 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1002 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 787 GLN C 957 GLN C 965 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.131343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.080059 restraints weight = 59664.934| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.65 r_work: 0.3101 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 28823 Z= 0.289 Angle : 0.752 11.639 39363 Z= 0.355 Chirality : 0.050 0.400 4638 Planarity : 0.004 0.068 4933 Dihedral : 9.728 109.158 5519 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.36 % Favored : 93.46 % Rotamer: Outliers : 2.69 % Allowed : 13.53 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3397 helix: 1.63 (0.18), residues: 802 sheet: -0.35 (0.21), residues: 625 loop : -1.23 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 105 HIS 0.005 0.001 HIS B 519 PHE 0.033 0.002 PHE B 166 TYR 0.026 0.002 TYR C 837 ARG 0.013 0.001 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 46) link_NAG-ASN : angle 2.74831 ( 138) link_BETA1-4 : bond 0.00707 ( 42) link_BETA1-4 : angle 2.76285 ( 126) hydrogen bonds : bond 0.04577 ( 960) hydrogen bonds : angle 5.46048 ( 2751) SS BOND : bond 0.00634 ( 42) SS BOND : angle 1.34851 ( 84) covalent geometry : bond 0.00676 (28692) covalent geometry : angle 0.71765 (39015) Misc. bond : bond 0.00635 ( 1) *********************** 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 241 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 161 time to evaluate : 2.734 Fit side-chains revert: symmetry clash REVERT: A 70 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7907 (m) REVERT: A 105 TRP cc_start: 0.8509 (m-90) cc_final: 0.8220 (m-10) REVERT: A 175 MET cc_start: 0.7925 (mmt) cc_final: 0.7147 (pmm) REVERT: A 342 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7891 (m-80) REVERT: A 408 ARG cc_start: 0.8229 (tpp-160) cc_final: 0.8016 (tpp-160) REVERT: A 421 TYR cc_start: 0.7140 (m-80) cc_final: 0.6864 (m-80) REVERT: A 756 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7888 (t80) REVERT: A 918 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8947 (pm20) REVERT: B 67 TRP cc_start: 0.8945 (t60) cc_final: 0.8537 (t-100) REVERT: B 619 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: B 751 ASN cc_start: 0.9322 (m110) cc_final: 0.8968 (m110) REVERT: B 855 PHE cc_start: 0.8204 (t80) cc_final: 0.7781 (t80) REVERT: C 33 ASN cc_start: 0.8706 (t0) cc_final: 0.8151 (t0) REVERT: C 193 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7966 (ttpt) REVERT: C 574 ASP cc_start: 0.7358 (t0) cc_final: 0.7158 (OUTLIER) REVERT: C 740 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8330 (ppp) REVERT: F 39 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8464 (pp30) outliers start: 80 outliers final: 34 residues processed: 220 average time/residue: 0.8203 time to fit residues: 233.3373 Evaluate side-chains 184 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 714 ILE 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 131 VAL Chi-restraints excluded: chain B residue 277 LEU 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 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 203 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 645 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 33 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 232 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 275 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 298 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 135 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.133498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.083548 restraints weight = 59381.648| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.70 r_work: 0.3174 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2471 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 : 0.661 11.952 39363 Z= 0.308 Chirality : 0.047 0.437 4638 Planarity : 0.004 0.063 4933 Dihedral : 9.098 111.000 5519 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.50 % Favored : 94.32 % Rotamer: Outliers : 1.51 % Allowed : 15.28 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3397 helix: 1.88 (0.19), residues: 795 sheet: -0.38 (0.21), residues: 644 loop : -1.17 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 105 HIS 0.005 0.001 HIS B 519 PHE 0.024 0.001 PHE B 93 TYR 0.020 0.001 TYR C1067 ARG 0.007 0.000 ARG F 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 46) link_NAG-ASN : angle 2.56930 ( 138) link_BETA1-4 : bond 0.00681 ( 42) link_BETA1-4 : angle 2.57347 ( 126) hydrogen bonds : bond 0.03782 ( 960) hydrogen bonds : angle 5.16116 ( 2751) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.12283 ( 84) covalent geometry : bond 0.00273 (28692) covalent geometry : angle 0.62698 (39015) Misc. bond : bond 0.00750 ( 1) *********************** 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 208 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 7.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7864 (m) REVERT: A 175 MET cc_start: 0.7756 (mmt) cc_final: 0.7104 (pmm) REVERT: A 342 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: A 421 TYR cc_start: 0.7155 (m-80) cc_final: 0.6894 (m-80) REVERT: A 902 MET cc_start: 0.9130 (tpp) cc_final: 0.8919 (mmm) REVERT: A 918 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8743 (pm20) REVERT: A 1138 TYR cc_start: 0.8848 (t80) cc_final: 0.8591 (t80) REVERT: B 67 TRP cc_start: 0.8954 (t60) cc_final: 0.8592 (t-100) REVERT: B 166 PHE cc_start: 0.7957 (t80) cc_final: 0.7751 (t80) REVERT: B 362 VAL cc_start: 0.6353 (OUTLIER) cc_final: 0.6122 (m) REVERT: B 751 ASN cc_start: 0.9301 (m110) cc_final: 0.8943 (m110) REVERT: B 855 PHE cc_start: 0.8235 (t80) cc_final: 0.7837 (t80) REVERT: B 1130 ILE cc_start: 0.9352 (pt) cc_final: 0.9138 (pp) REVERT: C 33 ASN cc_start: 0.8739 (t0) cc_final: 0.8126 (t0) REVERT: C 357 ARG cc_start: 0.6201 (tmm160) cc_final: 0.5927 (tmm-80) REVERT: C 740 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8157 (ppp) REVERT: F 31 ARG cc_start: 0.8052 (mpt-90) cc_final: 0.7793 (mpt-90) outliers start: 45 outliers final: 27 residues processed: 193 average time/residue: 0.9886 time to fit residues: 244.6297 Evaluate side-chains 180 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER 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 515 PHE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR 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 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 377 PHE 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 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 52 optimal weight: 10.0000 chunk 282 optimal weight: 0.6980 chunk 247 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 338 optimal weight: 2.9990 chunk 196 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 965 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.132623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.082787 restraints weight = 59456.615| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.65 r_work: 0.3168 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2559 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= 0.159 Angle : 0.667 11.881 39363 Z= 0.312 Chirality : 0.047 0.434 4638 Planarity : 0.004 0.064 4933 Dihedral : 8.885 110.431 5519 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.48 % Favored : 94.35 % Rotamer: Outliers : 2.02 % Allowed : 14.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3397 helix: 1.89 (0.19), residues: 795 sheet: -0.37 (0.21), residues: 642 loop : -1.16 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 105 HIS 0.016 0.001 HIS F 15 PHE 0.023 0.001 PHE B 93 TYR 0.021 0.001 TYR C 904 ARG 0.015 0.000 ARG F 35 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 46) link_NAG-ASN : angle 2.57074 ( 138) link_BETA1-4 : bond 0.00657 ( 42) link_BETA1-4 : angle 2.57410 ( 126) hydrogen bonds : bond 0.03849 ( 960) hydrogen bonds : angle 5.13764 ( 2751) SS BOND : bond 0.00250 ( 42) SS BOND : angle 1.12560 ( 84) covalent geometry : bond 0.00366 (28692) covalent geometry : angle 0.63358 (39015) Misc. bond : bond 0.00315 ( 1) *********************** 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 217 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 157 time to evaluate : 3.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7853 (m) REVERT: A 105 TRP cc_start: 0.8471 (m-90) cc_final: 0.8179 (m-10) REVERT: A 175 MET cc_start: 0.7816 (mmt) cc_final: 0.7004 (pmm) REVERT: A 342 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: A 421 TYR cc_start: 0.7159 (m-80) cc_final: 0.6900 (m-80) REVERT: A 918 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8666 (pm20) REVERT: A 1138 TYR cc_start: 0.8869 (t80) cc_final: 0.8591 (t80) REVERT: B 67 TRP cc_start: 0.8976 (t60) cc_final: 0.8579 (t-100) REVERT: B 362 VAL cc_start: 0.6376 (OUTLIER) cc_final: 0.6123 (m) REVERT: B 751 ASN cc_start: 0.9313 (m110) cc_final: 0.8957 (m110) REVERT: B 855 PHE cc_start: 0.8227 (t80) cc_final: 0.7806 (t80) REVERT: B 1130 ILE cc_start: 0.9358 (pt) cc_final: 0.9147 (pp) REVERT: C 33 ASN cc_start: 0.8745 (t0) cc_final: 0.8141 (t0) REVERT: C 193 LYS cc_start: 0.8344 (ttpt) cc_final: 0.8024 (ttpt) REVERT: C 357 ARG cc_start: 0.6192 (tmm160) cc_final: 0.5908 (tmm-80) REVERT: C 740 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8228 (ppp) REVERT: F 39 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8525 (pp30) outliers start: 60 outliers final: 34 residues processed: 200 average time/residue: 1.0149 time to fit residues: 257.2088 Evaluate side-chains 188 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER 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 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 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 666 ILE 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 C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 236 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 292 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 155 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.131162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081135 restraints weight = 59431.549| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.63 r_work: 0.3132 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2784 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= 0.219 Angle : 0.709 12.059 39363 Z= 0.333 Chirality : 0.048 0.432 4638 Planarity : 0.004 0.064 4933 Dihedral : 8.611 108.505 5519 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.74 % Favored : 94.08 % Rotamer: Outliers : 1.72 % Allowed : 15.38 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3397 helix: 1.80 (0.19), residues: 796 sheet: -0.41 (0.21), residues: 615 loop : -1.22 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 105 HIS 0.015 0.001 HIS F 15 PHE 0.040 0.002 PHE B 166 TYR 0.026 0.002 TYR B 904 ARG 0.010 0.001 ARG F 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 46) link_NAG-ASN : angle 2.69406 ( 138) link_BETA1-4 : bond 0.00659 ( 42) link_BETA1-4 : angle 2.62830 ( 126) hydrogen bonds : bond 0.04172 ( 960) hydrogen bonds : angle 5.25872 ( 2751) SS BOND : bond 0.00318 ( 42) SS BOND : angle 1.23845 ( 84) covalent geometry : bond 0.00511 (28692) covalent geometry : angle 0.67554 (39015) Misc. bond : bond 0.00380 ( 1) *********************** 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 205 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 8.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7862 (m) REVERT: A 175 MET cc_start: 0.7837 (mmt) cc_final: 0.6994 (ptp) REVERT: A 242 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8460 (mm) REVERT: A 342 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: A 421 TYR cc_start: 0.7136 (m-80) cc_final: 0.6870 (m-80) REVERT: A 918 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8780 (pm20) REVERT: B 67 TRP cc_start: 0.8999 (t60) cc_final: 0.8567 (t-100) REVERT: B 751 ASN cc_start: 0.9347 (m110) cc_final: 0.8989 (m110) REVERT: B 855 PHE cc_start: 0.8226 (t80) cc_final: 0.7815 (t80) REVERT: C 33 ASN cc_start: 0.8735 (t0) cc_final: 0.8165 (t0) REVERT: C 193 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7917 (ttpt) REVERT: C 357 ARG cc_start: 0.6208 (tmm160) cc_final: 0.5924 (tmm-80) REVERT: C 574 ASP cc_start: 0.7461 (t0) cc_final: 0.7193 (t0) REVERT: C 740 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8296 (ppp) REVERT: F 8 GLN cc_start: 0.7504 (pp30) cc_final: 0.7191 (mm110) outliers start: 51 outliers final: 35 residues processed: 194 average time/residue: 1.3906 time to fit residues: 359.2406 Evaluate side-chains 182 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 3.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 242 LEU 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 859 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 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 666 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 198 optimal weight: 0.6980 chunk 108 optimal weight: 0.2980 chunk 320 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 338 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4153 r_free = 0.4153 target = 0.134575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.084465 restraints weight = 58977.934| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.63 r_work: 0.3189 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28823 Z= 0.122 Angle : 0.665 13.444 39363 Z= 0.311 Chirality : 0.047 0.450 4638 Planarity : 0.004 0.051 4933 Dihedral : 8.185 105.786 5519 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.48 % Favored : 94.35 % Rotamer: Outliers : 1.48 % Allowed : 15.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3397 helix: 1.92 (0.19), residues: 803 sheet: -0.42 (0.21), residues: 642 loop : -1.17 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 105 HIS 0.019 0.001 HIS F 15 PHE 0.020 0.001 PHE B 456 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.000 ARG F 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 46) link_NAG-ASN : angle 2.57639 ( 138) link_BETA1-4 : bond 0.00640 ( 42) link_BETA1-4 : angle 2.48005 ( 126) hydrogen bonds : bond 0.03633 ( 960) hydrogen bonds : angle 5.05195 ( 2751) SS BOND : bond 0.00215 ( 42) SS BOND : angle 1.10613 ( 84) covalent geometry : bond 0.00269 (28692) covalent geometry : angle 0.63311 (39015) Misc. bond : bond 0.01421 ( 1) ********************** 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 208 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7754 (m) REVERT: A 175 MET cc_start: 0.7816 (mmt) cc_final: 0.7117 (ptp) REVERT: A 242 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 342 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: A 421 TYR cc_start: 0.7135 (m-80) cc_final: 0.6877 (m-80) REVERT: A 453 TYR cc_start: 0.6379 (p90) cc_final: 0.5875 (p90) REVERT: A 918 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8768 (pm20) REVERT: B 67 TRP cc_start: 0.8894 (t60) cc_final: 0.8477 (t-100) REVERT: B 354 ASN cc_start: 0.9074 (t0) cc_final: 0.8214 (p0) REVERT: B 362 VAL cc_start: 0.6361 (OUTLIER) cc_final: 0.6124 (m) REVERT: B 751 ASN cc_start: 0.9333 (m110) cc_final: 0.8975 (m110) REVERT: B 855 PHE cc_start: 0.8240 (t80) cc_final: 0.7841 (t80) REVERT: C 33 ASN cc_start: 0.8792 (t0) cc_final: 0.8195 (t0) REVERT: C 106 ILE cc_start: 0.8542 (pp) cc_final: 0.8321 (pp) REVERT: C 135 GLN cc_start: 0.8010 (tp40) cc_final: 0.7669 (pp30) REVERT: C 241 LEU cc_start: 0.8260 (mm) cc_final: 0.7319 (tp) REVERT: C 357 ARG cc_start: 0.6249 (tmm160) cc_final: 0.5961 (tmm-80) REVERT: C 574 ASP cc_start: 0.7235 (t0) cc_final: 0.7024 (t0) REVERT: C 740 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8177 (ppp) REVERT: C 902 MET cc_start: 0.9261 (tpt) cc_final: 0.9027 (mmm) REVERT: F 8 GLN cc_start: 0.7485 (pp30) cc_final: 0.7149 (mm110) outliers start: 44 outliers final: 34 residues processed: 196 average time/residue: 0.9234 time to fit residues: 229.3125 Evaluate side-chains 195 residues out of total 2981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 242 LEU 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 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 131 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 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 221 SER 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 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 285 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 106 optimal weight: 0.0030 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN F 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.135043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.084572 restraints weight = 59556.116| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.65 r_work: 0.3194 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2751 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= 0.120 Angle : 0.661 13.006 39363 Z= 0.307 Chirality : 0.046 0.441 4638 Planarity : 0.004 0.049 4933 Dihedral : 7.894 101.527 5519 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.39 % Favored : 94.44 % Rotamer: Outliers : 1.31 % Allowed : 16.22 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3397 helix: 1.97 (0.19), residues: 799 sheet: -0.33 (0.21), residues: 637 loop : -1.17 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 105 HIS 0.019 0.001 HIS F 15 PHE 0.035 0.001 PHE B 166 TYR 0.023 0.001 TYR C 904 ARG 0.008 0.000 ARG F 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 46) link_NAG-ASN : angle 2.53809 ( 138) link_BETA1-4 : bond 0.00633 ( 42) link_BETA1-4 : angle 2.41483 ( 126) hydrogen bonds : bond 0.03552 ( 960) hydrogen bonds : angle 4.95808 ( 2751) SS BOND : bond 0.00199 ( 42) SS BOND : angle 1.02424 ( 84) covalent geometry : bond 0.00266 (28692) covalent geometry : angle 0.63014 (39015) Misc. bond : bond 0.00149 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26155.69 seconds wall clock time: 460 minutes 11.31 seconds (27611.31 seconds total)