Starting phenix.real_space_refine on Mon Sep 14 08:49:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xvr_67300/09_2026/9xvr_67300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xvr_67300/09_2026/9xvr_67300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xvr_67300/09_2026/9xvr_67300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xvr_67300/09_2026/9xvr_67300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xvr_67300/09_2026/9xvr_67300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xvr_67300/09_2026/9xvr_67300.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.063 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 174 5.16 5 C 17934 2.51 5 N 4608 2.21 5 O 5745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28461 Number of models: 1 Model: "" Number of chains: 30 Chain: "B" Number of atoms: 9045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9045 Classifications: {'peptide': 1157} Link IDs: {'PTRANS': 44, 'TRANS': 1112} Chain breaks: 2 Chain: "A" Number of atoms: 9045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9045 Classifications: {'peptide': 1157} Link IDs: {'PTRANS': 44, 'TRANS': 1112} Chain breaks: 2 Chain: "C" Number of atoms: 9045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9045 Classifications: {'peptide': 1157} Link IDs: {'PTRANS': 44, 'TRANS': 1112} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 6.10, per 1000 atoms: 0.21 Number of scatterers: 28461 At special positions: 0 Unit cell: (159.43, 150.87, 159.43, 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 174 16.00 O 5745 8.00 N 4608 7.00 C 17934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 178 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 396 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 515 " distance=2.03 Simple disulfide: pdb=" SG CYS B 590 " - pdb=" SG CYS B 641 " distance=2.03 Simple disulfide: pdb=" SG CYS B 607 " - pdb=" SG CYS B 637 " distance=2.04 Simple disulfide: pdb=" SG CYS B 666 " - pdb=" SG CYS B 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 711 " - pdb=" SG CYS B 720 " distance=2.03 Simple disulfide: pdb=" SG CYS B 782 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 787 " - pdb=" SG CYS B 793 " distance=2.03 Simple disulfide: pdb=" SG CYS B 888 " - pdb=" SG CYS B 901 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1093 " distance=2.03 Simple disulfide: pdb=" SG CYS B1132 " - pdb=" SG CYS B1138 " distance=2.03 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 226 " distance=2.05 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 396 " distance=2.03 Simple disulfide: pdb=" SG CYS A 414 " - pdb=" SG CYS A 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 426 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 641 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 637 " distance=2.04 Simple disulfide: pdb=" SG CYS A 666 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 720 " distance=2.03 Simple disulfide: pdb=" SG CYS A 782 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS A 787 " - pdb=" SG CYS A 793 " distance=2.03 Simple disulfide: pdb=" SG CYS A 888 " - pdb=" SG CYS A 901 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1093 " distance=2.03 Simple disulfide: pdb=" SG CYS A1132 " - pdb=" SG CYS A1138 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 188 " distance=2.03 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 226 " distance=2.05 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 338 " distance=2.03 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 396 " distance=2.03 Simple disulfide: pdb=" SG CYS C 414 " - pdb=" SG CYS C 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 426 " - pdb=" SG CYS C 571 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 515 " distance=2.03 Simple disulfide: pdb=" SG CYS C 590 " - pdb=" SG CYS C 641 " distance=2.03 Simple disulfide: pdb=" SG CYS C 607 " - pdb=" SG CYS C 637 " distance=2.04 Simple disulfide: pdb=" SG CYS C 666 " - pdb=" SG CYS C 697 " distance=2.03 Simple disulfide: pdb=" SG CYS C 711 " - pdb=" SG CYS C 720 " distance=2.03 Simple disulfide: pdb=" SG CYS C 782 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 787 " - pdb=" SG CYS C 793 " distance=2.03 Simple disulfide: pdb=" SG CYS C 888 " - pdb=" SG CYS C 901 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1093 " distance=2.03 Simple disulfide: pdb=" SG CYS C1132 " - pdb=" SG CYS C1138 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 115 " " NAG A1403 " - " ASN A 152 " " NAG A1404 " - " ASN A 184 " " NAG A1405 " - " ASN A 202 " " NAG A1406 " - " ASN A 233 " " NAG A1407 " - " ASN A 476 " " NAG A1408 " - " ASN A 482 " " NAG A1409 " - " ASN A 608 " " NAG A1410 " - " ASN A 703 " " NAG A1411 " - " ASN A 761 " " NAG A1412 " - " ASN A 846 " " NAG A1413 " - " ASN A1124 " " NAG A1414 " - " ASN A1149 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 115 " " NAG B1403 " - " ASN B 152 " " NAG B1404 " - " ASN B 184 " " NAG B1405 " - " ASN B 202 " " NAG B1406 " - " ASN B 233 " " NAG B1407 " - " ASN B 476 " " NAG B1408 " - " ASN B 482 " " NAG B1409 " - " ASN B 608 " " NAG B1410 " - " ASN B 703 " " NAG B1411 " - " ASN B 761 " " NAG B1412 " - " ASN B 846 " " NAG B1413 " - " ASN B1124 " " NAG B1414 " - " ASN B1149 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 115 " " NAG C1403 " - " ASN C 152 " " NAG C1404 " - " ASN C 184 " " NAG C1405 " - " ASN C 202 " " NAG C1406 " - " ASN C 233 " " NAG C1407 " - " ASN C 476 " " NAG C1408 " - " ASN C 482 " " NAG C1409 " - " ASN C 608 " " NAG C1410 " - " ASN C 703 " " NAG C1411 " - " ASN C 761 " " NAG C1412 " - " ASN C 846 " " NAG C1413 " - " ASN C1124 " " NAG C1414 " - " ASN C1149 " " NAG D 1 " - " ASN B 31 " " NAG E 1 " - " ASN B 44 " " NAG F 1 " - " ASN B 94 " " NAG G 1 " - " ASN B 159 " " NAG H 1 " - " ASN B 289 " " NAG I 1 " - " ASN B 387 " " NAG J 1 " - " ASN B 399 " " NAG K 1 " - " ASN B1185 " " NAG L 1 " - " ASN A 31 " " NAG M 1 " - " ASN A 44 " " NAG N 1 " - " ASN A 94 " " NAG O 1 " - " ASN A 159 " " NAG P 1 " - " ASN A 289 " " NAG Q 1 " - " ASN A 387 " " NAG R 1 " - " ASN A 399 " " NAG S 1 " - " ASN A1185 " " NAG T 1 " - " ASN C 31 " " NAG U 1 " - " ASN C 44 " " NAG V 1 " - " ASN C 94 " " NAG W 1 " - " ASN C 159 " " NAG X 1 " - " ASN C 289 " " NAG Y 1 " - " ASN C 387 " " NAG Z 1 " - " ASN C 399 " " NAG a 1 " - " ASN C1185 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.0 seconds 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6480 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 61 sheets defined 25.6% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'B' and resid 32 through 36 removed outlier: 3.735A pdb=" N ILE B 36 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.501A pdb=" N ARG B 47 " --> pdb=" O ASN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.682A pdb=" N SER B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 341 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.597A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 removed outlier: 4.016A pdb=" N LEU B 403 " --> pdb=" O ASN B 399 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 424 removed outlier: 3.727A pdb=" N THR B 424 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 451 through 457 removed outlier: 3.768A pdb=" N MET B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 522 removed outlier: 3.521A pdb=" N LEU B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 586 removed outlier: 4.147A pdb=" N GLU B 585 " --> pdb=" O ASN B 582 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 586 " --> pdb=" O LEU B 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 582 through 586' Processing helix chain 'B' and resid 612 through 616 removed outlier: 3.574A pdb=" N ILE B 616 " --> pdb=" O ALA B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.672A pdb=" N ILE B 672 " --> pdb=" O HIS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 687 removed outlier: 3.733A pdb=" N SER B 682 " --> pdb=" O ARG B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 788 Processing helix chain 'B' and resid 790 through 797 Processing helix chain 'B' and resid 798 through 801 removed outlier: 3.657A pdb=" N GLY B 801 " --> pdb=" O GLU B 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 798 through 801' Processing helix chain 'B' and resid 806 through 826 Processing helix chain 'B' and resid 864 through 874 removed outlier: 3.539A pdb=" N VAL B 874 " --> pdb=" O LEU B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 892 removed outlier: 3.674A pdb=" N CYS B 888 " --> pdb=" O GLY B 884 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 891 " --> pdb=" O GLU B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 907 Processing helix chain 'B' and resid 916 through 931 removed outlier: 4.638A pdb=" N MET B 922 " --> pdb=" O ASN B 918 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 923 " --> pdb=" O MET B 919 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 925 " --> pdb=" O ALA B 921 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 958 Processing helix chain 'B' and resid 962 through 969 removed outlier: 3.535A pdb=" N LEU B 966 " --> pdb=" O THR B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 992 through 1014 removed outlier: 3.683A pdb=" N GLN B 999 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B1008 " --> pdb=" O ALA B1004 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B1009 " --> pdb=" O ASN B1005 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B1010 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B1012 " --> pdb=" O ALA B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1017 No H-bonds generated for 'chain 'B' and resid 1015 through 1017' Processing helix chain 'B' and resid 1026 through 1034 Processing helix chain 'B' and resid 1035 through 1078 removed outlier: 3.962A pdb=" N GLU B1040 " --> pdb=" O VAL B1036 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B1041 " --> pdb=" O LEU B1037 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B1042 " --> pdb=" O GLU B1038 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP B1044 " --> pdb=" O GLU B1040 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B1045 " --> pdb=" O VAL B1041 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B1052 " --> pdb=" O ASN B1048 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B1053 " --> pdb=" O GLY B1049 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B1054 " --> pdb=" O ARG B1050 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B1057 " --> pdb=" O SER B1053 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU B1066 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B1067 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B1071 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B1072 " --> pdb=" O ALA B1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.573A pdb=" N ILE A 36 " --> pdb=" O SER A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 212 through 218 removed outlier: 3.689A pdb=" N SER A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 341 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.559A pdb=" N LEU A 377 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 407 removed outlier: 4.030A pdb=" N LEU A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.720A pdb=" N THR A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 513 through 522 removed outlier: 3.527A pdb=" N LEU A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 586 removed outlier: 4.041A pdb=" N GLU A 585 " --> pdb=" O ASN A 582 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 586 " --> pdb=" O LEU A 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 582 through 586' Processing helix chain 'A' and resid 612 through 616 removed outlier: 3.591A pdb=" N ILE A 616 " --> pdb=" O ALA A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 673 removed outlier: 4.463A pdb=" N SER A 671 " --> pdb=" O ASN A 667 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 672 " --> pdb=" O HIS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 removed outlier: 3.757A pdb=" N SER A 682 " --> pdb=" O ARG A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 788 Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 798 through 801 removed outlier: 3.673A pdb=" N GLY A 801 " --> pdb=" O GLU A 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 798 through 801' Processing helix chain 'A' and resid 806 through 826 Processing helix chain 'A' and resid 864 through 874 removed outlier: 3.562A pdb=" N VAL A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 892 removed outlier: 3.628A pdb=" N CYS A 888 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 907 Processing helix chain 'A' and resid 916 through 931 removed outlier: 4.628A pdb=" N MET A 922 " --> pdb=" O ASN A 918 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 923 " --> pdb=" O MET A 919 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 925 " --> pdb=" O ALA A 921 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 958 Processing helix chain 'A' and resid 962 through 969 removed outlier: 3.549A pdb=" N LEU A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 981 Processing helix chain 'A' and resid 992 through 1014 removed outlier: 3.646A pdb=" N GLN A 999 " --> pdb=" O PHE A 995 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A1014 " --> pdb=" O SER A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1026 through 1034 Processing helix chain 'A' and resid 1035 through 1078 removed outlier: 3.916A pdb=" N GLU A1040 " --> pdb=" O VAL A1036 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A1042 " --> pdb=" O GLU A1038 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP A1044 " --> pdb=" O GLU A1040 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A1052 " --> pdb=" O ASN A1048 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A1053 " --> pdb=" O GLY A1049 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1054 " --> pdb=" O ARG A1050 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A1067 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A1069 " --> pdb=" O SER A1065 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A1071 " --> pdb=" O ALA A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1172 No H-bonds generated for 'chain 'A' and resid 1170 through 1172' Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.699A pdb=" N ILE C 36 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 212 through 218 removed outlier: 3.692A pdb=" N SER C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 341 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.552A pdb=" N LEU C 377 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 407 removed outlier: 4.013A pdb=" N LEU C 403 " --> pdb=" O ASN C 399 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C 406 " --> pdb=" O LYS C 402 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 424 removed outlier: 3.727A pdb=" N THR C 424 " --> pdb=" O GLU C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 removed outlier: 4.903A pdb=" N SER C 443 " --> pdb=" O SER C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 513 through 522 removed outlier: 3.539A pdb=" N LEU C 520 " --> pdb=" O ARG C 516 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 522 " --> pdb=" O GLY C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 removed outlier: 3.650A pdb=" N ILE C 616 " --> pdb=" O ALA C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 673 removed outlier: 3.612A pdb=" N ILE C 672 " --> pdb=" O HIS C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 687 removed outlier: 3.717A pdb=" N SER C 682 " --> pdb=" O ARG C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 788 Processing helix chain 'C' and resid 790 through 797 Processing helix chain 'C' and resid 798 through 801 removed outlier: 3.705A pdb=" N GLY C 801 " --> pdb=" O GLU C 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 798 through 801' Processing helix chain 'C' and resid 806 through 826 Processing helix chain 'C' and resid 864 through 874 removed outlier: 3.573A pdb=" N VAL C 874 " --> pdb=" O LEU C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 892 removed outlier: 3.636A pdb=" N CYS C 888 " --> pdb=" O GLY C 884 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 891 " --> pdb=" O GLU C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 916 through 931 removed outlier: 4.630A pdb=" N MET C 922 " --> pdb=" O ASN C 918 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR C 923 " --> pdb=" O MET C 919 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 925 " --> pdb=" O ALA C 921 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 959 removed outlier: 3.895A pdb=" N ILE C 959 " --> pdb=" O ARG C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 969 removed outlier: 3.537A pdb=" N LEU C 966 " --> pdb=" O THR C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 981 Processing helix chain 'C' and resid 992 through 1014 removed outlier: 3.632A pdb=" N GLN C 999 " --> pdb=" O PHE C 995 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C1009 " --> pdb=" O ASN C1005 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C1010 " --> pdb=" O ALA C1006 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1017 No H-bonds generated for 'chain 'C' and resid 1015 through 1017' Processing helix chain 'C' and resid 1026 through 1034 Processing helix chain 'C' and resid 1035 through 1078 removed outlier: 3.907A pdb=" N GLU C1040 " --> pdb=" O VAL C1036 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL C1041 " --> pdb=" O LEU C1037 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C1042 " --> pdb=" O GLU C1038 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP C1044 " --> pdb=" O GLU C1040 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C1045 " --> pdb=" O VAL C1041 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C1052 " --> pdb=" O ASN C1048 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C1053 " --> pdb=" O GLY C1049 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C1054 " --> pdb=" O ARG C1050 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C1057 " --> pdb=" O SER C1053 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU C1066 " --> pdb=" O LEU C1062 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C1067 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C1069 " --> pdb=" O SER C1065 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C1071 " --> pdb=" O ALA C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1170 through 1172 No H-bonds generated for 'chain 'C' and resid 1170 through 1172' Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 30 removed outlier: 6.619A pdb=" N GLU B 29 " --> pdb=" O ILE B 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 70 removed outlier: 6.833A pdb=" N ASP B 315 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.607A pdb=" N ALA B 270 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR B 256 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 268 " --> pdb=" O THR B 256 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.977A pdb=" N SER B 83 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU B 199 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN B 289 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU B 201 " --> pdb=" O ASN B 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 101 removed outlier: 3.807A pdb=" N TYR B 281 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER B 143 " --> pdb=" O HIS B 160 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N HIS B 160 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 145 " --> pdb=" O PHE B 158 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE B 158 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS B 147 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ALA B 156 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 117 through 118 removed outlier: 3.605A pdb=" N GLY B 130 " --> pdb=" O GLY B 118 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA B 298 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 182 removed outlier: 3.952A pdb=" N LYS B 224 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 351 removed outlier: 3.598A pdb=" N MET B 656 " --> pdb=" O ASP B 651 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.838A pdb=" N ASP B 592 " --> pdb=" O GLY B 361 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 365 " --> pdb=" O ASP B 594 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 602 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B 593 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 389 through 393 removed outlier: 3.801A pdb=" N SER B 389 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER B 429 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP B 433 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 559 " --> pdb=" O CYS B 467 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU B 411 " --> pdb=" O HIS B 470 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AB3, first strand: chain 'B' and resid 490 through 494 removed outlier: 5.574A pdb=" N GLY B 541 " --> pdb=" O SER B 493 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 548 through 549 Processing sheet with id=AB5, first strand: chain 'B' and resid 628 through 629 Processing sheet with id=AB6, first strand: chain 'B' and resid 701 through 707 removed outlier: 3.502A pdb=" N THR B 704 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLN B 737 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLU B 706 " --> pdb=" O GLN B 737 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 767 through 771 removed outlier: 3.518A pdb=" N VAL B1100 " --> pdb=" O VAL B1115 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR B1117 " --> pdb=" O HIS B1098 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS B1098 " --> pdb=" O TYR B1117 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 767 through 771 removed outlier: 6.265A pdb=" N TYR B1122 " --> pdb=" O PRO B 759 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASN B1124 " --> pdb=" O SER B 757 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER B 757 " --> pdb=" O ASN B1124 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 943 " --> pdb=" O SER B 757 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 778 through 780 Processing sheet with id=AC1, first strand: chain 'B' and resid 943 through 944 removed outlier: 3.681A pdb=" N ALA B 943 " --> pdb=" O SER C 757 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER C 757 " --> pdb=" O ASN C1124 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASN C1124 " --> pdb=" O SER C 757 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR C1122 " --> pdb=" O PRO C 759 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 943 through 944 removed outlier: 3.681A pdb=" N ALA B 943 " --> pdb=" O SER C 757 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER C 757 " --> pdb=" O ASN C1124 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASN C1124 " --> pdb=" O SER C 757 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR C1122 " --> pdb=" O PRO C 759 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C1100 " --> pdb=" O VAL C1115 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR C1117 " --> pdb=" O HIS C1098 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N HIS C1098 " --> pdb=" O TYR C1117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1131 through 1132 Processing sheet with id=AC4, first strand: chain 'B' and resid 1138 through 1141 removed outlier: 4.116A pdb=" N CYS B1138 " --> pdb=" O VAL B1177 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1144 through 1148 Processing sheet with id=AC6, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.560A pdb=" N GLU A 29 " --> pdb=" O ILE A 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 63 through 70 removed outlier: 6.891A pdb=" N ASP A 315 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 78 through 80 removed outlier: 3.618A pdb=" N ALA A 270 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR A 256 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU A 268 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.045A pdb=" N SER A 83 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 199 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASN A 289 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU A 201 " --> pdb=" O ASN A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 100 through 101 removed outlier: 3.765A pdb=" N TYR A 281 " --> pdb=" O GLN A 100 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 143 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N HIS A 160 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 145 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE A 158 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS A 147 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA A 156 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.638A pdb=" N GLY A 130 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA A 298 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 179 through 182 removed outlier: 3.921A pdb=" N LYS A 224 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 348 through 349 removed outlier: 3.610A pdb=" N MET A 656 " --> pdb=" O ASP A 651 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 362 through 365 removed outlier: 4.059A pdb=" N GLU A 365 " --> pdb=" O ASP A 594 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 602 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A 593 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.838A pdb=" N SER A 389 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP A 434 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 429 " --> pdb=" O THR A 562 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 433 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 559 " --> pdb=" O CYS A 467 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU A 411 " --> pdb=" O HIS A 470 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AD8, first strand: chain 'A' and resid 490 through 494 removed outlier: 5.537A pdb=" N GLY A 541 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 548 through 549 Processing sheet with id=AE1, first strand: chain 'A' and resid 628 through 629 Processing sheet with id=AE2, first strand: chain 'A' and resid 701 through 707 removed outlier: 3.520A pdb=" N THR A 704 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLN A 737 " --> pdb=" O THR A 704 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU A 706 " --> pdb=" O GLN A 737 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 767 through 771 removed outlier: 3.683A pdb=" N ALA A1106 " --> pdb=" O GLY A1109 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A1100 " --> pdb=" O VAL A1115 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR A1117 " --> pdb=" O HIS A1098 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS A1098 " --> pdb=" O TYR A1117 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 767 through 771 removed outlier: 6.236A pdb=" N TYR A1122 " --> pdb=" O PRO A 759 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASN A1124 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 757 " --> pdb=" O ASN A1124 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 943 " --> pdb=" O SER A 757 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 778 through 780 Processing sheet with id=AE6, first strand: chain 'A' and resid 1131 through 1132 Processing sheet with id=AE7, first strand: chain 'A' and resid 1139 through 1141 Processing sheet with id=AE8, first strand: chain 'A' and resid 1144 through 1148 Processing sheet with id=AE9, first strand: chain 'C' and resid 29 through 30 removed outlier: 6.648A pdb=" N GLU C 29 " --> pdb=" O ILE C 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 63 through 70 removed outlier: 6.966A pdb=" N ASP C 315 " --> pdb=" O THR C 323 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 78 through 80 removed outlier: 3.621A pdb=" N ALA C 270 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR C 256 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LEU C 268 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 83 through 84 removed outlier: 7.049A pdb=" N SER C 83 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU C 199 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASN C 289 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLU C 201 " --> pdb=" O ASN C 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 100 through 101 removed outlier: 3.824A pdb=" N TYR C 281 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER C 143 " --> pdb=" O HIS C 160 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N HIS C 160 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 145 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE C 158 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS C 147 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ALA C 156 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.651A pdb=" N GLY C 130 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA C 298 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 179 through 182 removed outlier: 3.957A pdb=" N LYS C 224 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 348 through 349 removed outlier: 3.509A pdb=" N ILE C 649 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET C 656 " --> pdb=" O ASP C 651 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 362 through 365 removed outlier: 4.095A pdb=" N GLU C 365 " --> pdb=" O ASP C 594 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 593 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 391 through 393 removed outlier: 3.903A pdb=" N SER C 429 " --> pdb=" O THR C 562 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP C 433 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 559 " --> pdb=" O CYS C 467 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU C 411 " --> pdb=" O HIS C 470 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 397 through 398 Processing sheet with id=AG2, first strand: chain 'C' and resid 490 through 494 removed outlier: 5.459A pdb=" N GLY C 541 " --> pdb=" O SER C 493 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 628 through 629 Processing sheet with id=AG4, first strand: chain 'C' and resid 701 through 707 removed outlier: 3.553A pdb=" N THR C 704 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN C 737 " --> pdb=" O THR C 704 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU C 706 " --> pdb=" O GLN C 737 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 778 through 780 Processing sheet with id=AG6, first strand: chain 'C' and resid 1174 through 1176 Processing sheet with id=AG7, first strand: chain 'C' and resid 1144 through 1148 848 hydrogen bonds defined for protein. 2289 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.45 Time building geometry restraints manager: 2.60 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: 9001 1.34 - 1.47: 7586 1.47 - 1.59: 12249 1.59 - 1.72: 0 1.72 - 1.84: 246 Bond restraints: 29082 Sorted by residual: bond pdb=" C GLU B1167 " pdb=" N PRO B1168 " ideal model delta sigma weight residual 1.330 1.360 -0.030 1.22e-02 6.72e+03 5.98e+00 bond pdb=" CA PRO B1168 " pdb=" C PRO B1168 " ideal model delta sigma weight residual 1.521 1.496 0.024 1.25e-02 6.40e+03 3.76e+00 bond pdb=" CB CYS B 782 " pdb=" SG CYS B 782 " ideal model delta sigma weight residual 1.808 1.747 0.061 3.30e-02 9.18e+02 3.43e+00 bond pdb=" CB CYS B 804 " pdb=" SG CYS B 804 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 3.02e+00 bond pdb=" CB CYS A 782 " pdb=" SG CYS A 782 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 3.01e+00 ... (remaining 29077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 38799 2.36 - 4.72: 583 4.72 - 7.08: 80 7.08 - 9.44: 4 9.44 - 11.80: 2 Bond angle restraints: 39468 Sorted by residual: angle pdb=" C ALA B 56 " pdb=" CA ALA B 56 " pdb=" CB ALA B 56 " ideal model delta sigma weight residual 116.63 110.41 6.22 1.16e+00 7.43e-01 2.88e+01 angle pdb=" CA GLU A 451 " pdb=" CB GLU A 451 " pdb=" CG GLU A 451 " ideal model delta sigma weight residual 114.10 124.50 -10.40 2.00e+00 2.50e-01 2.71e+01 angle pdb=" C ALA C 56 " pdb=" CA ALA C 56 " pdb=" CB ALA C 56 " ideal model delta sigma weight residual 117.23 110.33 6.90 1.36e+00 5.41e-01 2.58e+01 angle pdb=" C ALA A 56 " pdb=" CA ALA A 56 " pdb=" CB ALA A 56 " ideal model delta sigma weight residual 117.23 110.38 6.85 1.36e+00 5.41e-01 2.54e+01 angle pdb=" C CYS B 641 " pdb=" N VAL B 642 " pdb=" CA VAL B 642 " ideal model delta sigma weight residual 121.97 129.40 -7.43 1.80e+00 3.09e-01 1.70e+01 ... (remaining 39463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 16374 21.88 - 43.75: 1779 43.75 - 65.63: 321 65.63 - 87.51: 93 87.51 - 109.38: 33 Dihedral angle restraints: 18600 sinusoidal: 8451 harmonic: 10149 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1093 " pdb=" CB CYS A1093 " ideal model delta sinusoidal sigma weight residual -86.00 -176.19 90.19 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1093 " pdb=" CB CYS B1093 " ideal model delta sinusoidal sigma weight residual -86.00 -176.13 90.13 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1093 " pdb=" CB CYS C1093 " ideal model delta sinusoidal sigma weight residual 93.00 -176.92 -90.08 1 1.00e+01 1.00e-02 9.61e+01 ... (remaining 18597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 4560 0.135 - 0.269: 46 0.269 - 0.404: 8 0.404 - 0.538: 0 0.538 - 0.673: 3 Chirality restraints: 4617 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 159 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 159 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.55e+00 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN C 159 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.57e+00 ... (remaining 4614 not shown) Planarity restraints: 5061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 451 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" CD GLU A 451 " -0.044 2.00e-02 2.50e+03 pdb=" OE1 GLU A 451 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU A 451 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 159 " 0.019 2.00e-02 2.50e+03 1.83e-02 4.18e+00 pdb=" CG ASN B 159 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B 159 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 159 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 159 " 0.018 2.00e-02 2.50e+03 1.72e-02 3.68e+00 pdb=" CG ASN A 159 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 159 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 159 " -0.023 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.020 2.00e-02 2.50e+03 ... (remaining 5058 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 430 2.65 - 3.21: 25192 3.21 - 3.77: 40661 3.77 - 4.34: 57302 4.34 - 4.90: 96074 Nonbonded interactions: 219659 Sorted by model distance: nonbonded pdb=" O SER A 930 " pdb=" N ALA A 932 " model vdw 2.084 3.120 nonbonded pdb=" O SER B 930 " pdb=" N ALA B 932 " model vdw 2.084 3.120 nonbonded pdb=" O SER C 930 " pdb=" N ALA C 932 " model vdw 2.084 3.120 nonbonded pdb=" OG SER A 718 " pdb=" OD1 ASP C 916 " model vdw 2.137 3.040 nonbonded pdb=" OG SER A 443 " pdb=" O ASP C 410 " model vdw 2.163 3.040 ... (remaining 219654 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'Q' selection = chain 'R' selection = chain 'Y' selection = chain 'Z' } 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.240 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 0.061 29229 Z= 0.202 Angle : 0.729 11.797 39858 Z= 0.379 Chirality : 0.051 0.673 4617 Planarity : 0.003 0.045 4995 Dihedral : 18.002 109.385 11967 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.18 % Favored : 94.44 % Rotamer: Outliers : 0.27 % Allowed : 26.73 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.13), residues: 3453 helix: -0.50 (0.20), residues: 729 sheet: -0.26 (0.21), residues: 591 loop : -1.67 (0.12), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 360 TYR 0.028 0.001 TYR C 330 PHE 0.027 0.001 PHE C 948 TRP 0.009 0.001 TRP C 293 HIS 0.012 0.001 HIS B1171 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (29082) covalent geometry : angle 0.70968 / 0.37 (39468) SS BOND : bond 0.00464 / 0.25 ( 51) SS BOND : angle 1.76584 / 1.26 ( 102) hydrogen bonds : bond 0.24439 / 16.13 ( 831) hydrogen bonds : angle 9.40608 / 6.43 ( 2289) link_BETA1-4 : bond 0.00483 / 0.28 ( 30) link_BETA1-4 : angle 1.92475 / 1.30 ( 90) link_NAG-ASN : bond 0.00290 / 0.20 ( 66) link_NAG-ASN : angle 1.85520 / 1.29 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 286 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 LYS cc_start: 0.6027 (tttt) cc_final: 0.5708 (tttm) REVERT: B 360 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7838 (ttm-80) REVERT: B 539 TYR cc_start: 0.8697 (m-80) cc_final: 0.8474 (m-80) REVERT: B 945 SER cc_start: 0.8762 (t) cc_final: 0.8442 (p) REVERT: A 952 MET cc_start: 0.8639 (mmm) cc_final: 0.8335 (tpp) REVERT: A 967 MET cc_start: 0.8548 (mmp) cc_final: 0.8090 (mtt) REVERT: A 1095 LYS cc_start: 0.8767 (mttp) cc_final: 0.8525 (mtmm) REVERT: C 79 MET cc_start: 0.8681 (tmm) cc_final: 0.8326 (tmm) REVERT: C 364 TYR cc_start: 0.8991 (t80) cc_final: 0.8662 (t80) REVERT: C 410 ASP cc_start: 0.7472 (p0) cc_final: 0.7231 (p0) REVERT: C 1159 THR cc_start: 0.9089 (t) cc_final: 0.8862 (p) outliers start: 8 outliers final: 1 residues processed: 291 average time/residue: 0.1919 time to fit residues: 90.7816 Evaluate side-chains 263 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 511 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 356 ASN B1184 GLN A 356 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN C 833 GLN C 950 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108737 restraints weight = 42673.305| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.91 r_work: 0.3158 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29229 Z= 0.132 Angle : 0.628 10.256 39858 Z= 0.318 Chirality : 0.046 0.283 4617 Planarity : 0.004 0.040 4995 Dihedral : 9.044 62.632 5785 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.92 % Favored : 94.73 % Rotamer: Outliers : 3.43 % Allowed : 24.03 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.14), residues: 3453 helix: -0.26 (0.20), residues: 741 sheet: -0.22 (0.20), residues: 645 loop : -1.58 (0.12), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 360 TYR 0.017 0.001 TYR A 491 PHE 0.017 0.001 PHE B 754 TRP 0.008 0.001 TRP B 434 HIS 0.007 0.001 HIS A1171 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (29082) covalent geometry : angle 0.60938 / 0.31 (39468) SS BOND : bond 0.00310 / 0.20 ( 51) SS BOND : angle 1.40035 / 1.02 ( 102) hydrogen bonds : bond 0.04161 / 2.75 ( 831) hydrogen bonds : angle 6.18153 / 4.23 ( 2289) link_BETA1-4 : bond 0.00552 / 0.32 ( 30) link_BETA1-4 : angle 1.92553 / 1.31 ( 90) link_NAG-ASN : bond 0.00357 / 0.25 ( 66) link_NAG-ASN : angle 1.62851 / 1.13 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 292 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TYR cc_start: 0.8553 (m-80) cc_final: 0.8300 (m-80) REVERT: B 116 LYS cc_start: 0.6338 (tttt) cc_final: 0.6045 (tttm) REVERT: B 945 SER cc_start: 0.8733 (t) cc_final: 0.8439 (p) REVERT: B 973 ILE cc_start: 0.8476 (mm) cc_final: 0.8231 (mt) REVERT: B 1042 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: A 410 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7674 (p0) REVERT: A 510 MET cc_start: 0.8906 (mmm) cc_final: 0.8703 (mmm) REVERT: A 889 MET cc_start: 0.5952 (tpp) cc_final: 0.5688 (tpp) REVERT: A 956 MET cc_start: 0.8564 (ttp) cc_final: 0.8354 (ttp) REVERT: A 973 ILE cc_start: 0.8476 (mm) cc_final: 0.8233 (mt) REVERT: A 1146 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.6941 (m-80) REVERT: A 1157 PHE cc_start: 0.8600 (m-80) cc_final: 0.8265 (m-80) REVERT: C 79 MET cc_start: 0.8680 (tmm) cc_final: 0.8469 (tmm) REVERT: C 157 TYR cc_start: 0.8992 (m-80) cc_final: 0.8722 (m-80) REVERT: C 364 TYR cc_start: 0.8978 (t80) cc_final: 0.8622 (t80) REVERT: C 400 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8959 (mp) REVERT: C 1146 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7701 (m-80) outliers start: 103 outliers final: 39 residues processed: 390 average time/residue: 0.1789 time to fit residues: 114.4472 Evaluate side-chains 309 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1126 THR Chi-restraints excluded: chain B residue 1174 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1146 PHE Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 945 SER Chi-restraints excluded: chain C residue 998 VAL Chi-restraints excluded: chain C residue 1146 PHE Chi-restraints excluded: chain C residue 1154 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 258 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 333 optimal weight: 0.6980 chunk 257 optimal weight: 0.9980 chunk 306 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 296 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 HIS B1171 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.139092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.105529 restraints weight = 41782.063| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.94 r_work: 0.3088 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29229 Z= 0.132 Angle : 0.603 10.792 39858 Z= 0.304 Chirality : 0.046 0.382 4617 Planarity : 0.004 0.045 4995 Dihedral : 7.519 58.180 5785 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.15 % Favored : 94.56 % Rotamer: Outliers : 4.17 % Allowed : 23.13 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3453 helix: -0.03 (0.20), residues: 738 sheet: -0.12 (0.20), residues: 645 loop : -1.54 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.023 0.001 TYR A 194 PHE 0.016 0.001 PHE A 439 TRP 0.007 0.001 TRP B 434 HIS 0.010 0.001 HIS B1171 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (29082) covalent geometry : angle 0.58328 / 0.30 (39468) SS BOND : bond 0.00331 / 0.22 ( 51) SS BOND : angle 1.45768 / 1.05 ( 102) hydrogen bonds : bond 0.03803 / 2.51 ( 831) hydrogen bonds : angle 5.67730 / 3.86 ( 2289) link_BETA1-4 : bond 0.00532 / 0.32 ( 30) link_BETA1-4 : angle 1.88341 / 1.29 ( 90) link_NAG-ASN : bond 0.00248 / 0.17 ( 66) link_NAG-ASN : angle 1.61917 / 1.11 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 299 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 LYS cc_start: 0.5893 (tttt) cc_final: 0.5614 (tttm) REVERT: B 400 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8791 (mp) REVERT: B 439 PHE cc_start: 0.7922 (m-10) cc_final: 0.7643 (m-80) REVERT: B 945 SER cc_start: 0.8638 (t) cc_final: 0.8238 (p) REVERT: B 952 MET cc_start: 0.8469 (mmm) cc_final: 0.8152 (tpp) REVERT: B 973 ILE cc_start: 0.8250 (mm) cc_final: 0.8042 (mt) REVERT: B 1042 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: B 1080 ASN cc_start: 0.8935 (m-40) cc_final: 0.8705 (m110) REVERT: B 1175 ARG cc_start: 0.7644 (tmm160) cc_final: 0.7322 (ptm-80) REVERT: A 172 VAL cc_start: 0.8881 (t) cc_final: 0.8514 (p) REVERT: A 183 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7567 (mtpp) REVERT: A 189 THR cc_start: 0.7936 (OUTLIER) cc_final: 0.7732 (p) REVERT: A 360 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7926 (ttm110) REVERT: A 400 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8687 (tp) REVERT: A 476 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8067 (m-40) REVERT: A 510 MET cc_start: 0.8834 (mmm) cc_final: 0.8592 (mmm) REVERT: A 690 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6934 (t80) REVERT: A 869 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7928 (tp) REVERT: A 1007 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: A 1146 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.6675 (m-80) REVERT: A 1157 PHE cc_start: 0.8564 (m-80) cc_final: 0.8118 (m-80) REVERT: C 47 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8026 (mtm110) REVERT: C 82 TYR cc_start: 0.8700 (m-80) cc_final: 0.8412 (m-80) REVERT: C 157 TYR cc_start: 0.8951 (m-80) cc_final: 0.8658 (m-80) REVERT: C 194 TYR cc_start: 0.7907 (t80) cc_final: 0.7633 (t80) REVERT: C 364 TYR cc_start: 0.8899 (t80) cc_final: 0.8520 (t80) REVERT: C 400 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8798 (mp) REVERT: C 516 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7268 (ttt180) REVERT: C 1007 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7509 (mt0) REVERT: C 1146 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7473 (m-80) outliers start: 125 outliers final: 67 residues processed: 412 average time/residue: 0.1673 time to fit residues: 112.9869 Evaluate side-chains 353 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 271 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1126 THR Chi-restraints excluded: chain B residue 1174 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1146 PHE Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 187 TYR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 903 GLN Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 945 SER Chi-restraints excluded: chain C residue 998 VAL Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1041 VAL Chi-restraints excluded: chain C residue 1146 PHE Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1174 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 173 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 323 optimal weight: 7.9990 chunk 342 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 305 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1171 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102901 restraints weight = 42063.285| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.09 r_work: 0.3026 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 29229 Z= 0.188 Angle : 0.640 11.349 39858 Z= 0.322 Chirality : 0.047 0.331 4617 Planarity : 0.004 0.046 4995 Dihedral : 6.951 57.003 5785 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.79 % Favored : 93.95 % Rotamer: Outliers : 5.00 % Allowed : 23.47 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.14), residues: 3453 helix: -0.04 (0.20), residues: 738 sheet: -0.24 (0.20), residues: 645 loop : -1.56 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 358 TYR 0.017 0.002 TYR B 388 PHE 0.018 0.001 PHE A 439 TRP 0.009 0.001 TRP B 434 HIS 0.010 0.001 HIS B1171 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (29082) covalent geometry : angle 0.61707 / 0.32 (39468) SS BOND : bond 0.00448 / 0.30 ( 51) SS BOND : angle 1.81323 / 1.37 ( 102) hydrogen bonds : bond 0.03931 / 2.62 ( 831) hydrogen bonds : angle 5.51108 / 3.75 ( 2289) link_BETA1-4 : bond 0.00546 / 0.33 ( 30) link_BETA1-4 : angle 1.89872 / 1.28 ( 90) link_NAG-ASN : bond 0.00248 / 0.17 ( 66) link_NAG-ASN : angle 1.77426 / 1.20 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 271 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 315 ASP cc_start: 0.8556 (t70) cc_final: 0.8331 (t0) REVERT: B 400 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8783 (mp) REVERT: B 410 ASP cc_start: 0.8152 (p0) cc_final: 0.7543 (p0) REVERT: B 451 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8076 (pm20) REVERT: B 690 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6974 (t80) REVERT: B 945 SER cc_start: 0.8716 (t) cc_final: 0.8275 (p) REVERT: B 973 ILE cc_start: 0.8378 (mm) cc_final: 0.8147 (mt) REVERT: A 183 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7575 (mtpp) REVERT: A 269 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.7655 (p90) REVERT: A 311 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8168 (t0) REVERT: A 476 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8051 (m-40) REVERT: A 616 ILE cc_start: 0.8374 (mp) cc_final: 0.8134 (mm) REVERT: A 690 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7142 (t80) REVERT: A 869 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7917 (tp) REVERT: A 919 MET cc_start: 0.9020 (tmm) cc_final: 0.8564 (ttt) REVERT: A 1007 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: A 1146 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: A 1157 PHE cc_start: 0.8627 (m-80) cc_final: 0.8173 (m-80) REVERT: C 57 ARG cc_start: 0.7979 (ptm-80) cc_final: 0.7586 (ptm160) REVERT: C 239 ARG cc_start: 0.6232 (mmt180) cc_final: 0.6008 (mpt180) REVERT: C 269 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8403 (p90) REVERT: C 346 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7493 (t0) REVERT: C 364 TYR cc_start: 0.8902 (t80) cc_final: 0.8534 (t80) REVERT: C 952 MET cc_start: 0.8531 (tpp) cc_final: 0.8203 (tpp) REVERT: C 1146 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: C 1175 ARG cc_start: 0.7753 (tmm160) cc_final: 0.7536 (tmm160) outliers start: 150 outliers final: 94 residues processed: 405 average time/residue: 0.1890 time to fit residues: 125.3274 Evaluate side-chains 366 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 258 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 968 GLU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1019 THR Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1174 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1146 PHE Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 831 VAL Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 945 SER Chi-restraints excluded: chain C residue 998 VAL Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1041 VAL Chi-restraints excluded: chain C residue 1146 PHE Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1159 THR Chi-restraints excluded: chain C residue 1174 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 66 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 326 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 339 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 156 optimal weight: 0.2980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1080 ASN B1171 HIS A 356 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103522 restraints weight = 42077.257| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.93 r_work: 0.3028 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 29229 Z= 0.172 Angle : 0.620 11.727 39858 Z= 0.311 Chirality : 0.046 0.311 4617 Planarity : 0.004 0.048 4995 Dihedral : 6.653 56.136 5785 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.39 % Favored : 94.35 % Rotamer: Outliers : 5.07 % Allowed : 23.50 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3453 helix: -0.05 (0.20), residues: 738 sheet: -0.23 (0.20), residues: 645 loop : -1.53 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 358 TYR 0.021 0.001 TYR C 194 PHE 0.018 0.001 PHE B 269 TRP 0.009 0.001 TRP B 434 HIS 0.010 0.001 HIS B1171 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (29082) covalent geometry : angle 0.59795 / 0.31 (39468) SS BOND : bond 0.00428 / 0.25 ( 51) SS BOND : angle 1.70752 / 1.28 ( 102) hydrogen bonds : bond 0.03706 / 2.46 ( 831) hydrogen bonds : angle 5.40624 / 3.68 ( 2289) link_BETA1-4 : bond 0.00525 / 0.31 ( 30) link_BETA1-4 : angle 1.83253 / 1.24 ( 90) link_NAG-ASN : bond 0.00254 / 0.18 ( 66) link_NAG-ASN : angle 1.73957 / 1.18 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 281 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TYR cc_start: 0.8664 (m-80) cc_final: 0.8358 (m-80) REVERT: B 183 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7710 (mtpp) REVERT: B 315 ASP cc_start: 0.8558 (t70) cc_final: 0.8335 (t0) REVERT: B 400 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8777 (mp) REVERT: B 451 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: B 690 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.7197 (t80) REVERT: B 803 PHE cc_start: 0.8231 (t80) cc_final: 0.7782 (t80) REVERT: B 945 SER cc_start: 0.8653 (t) cc_final: 0.8193 (p) REVERT: B 973 ILE cc_start: 0.8397 (mm) cc_final: 0.8188 (mt) REVERT: B 1042 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: B 1175 ARG cc_start: 0.7701 (tmm160) cc_final: 0.7340 (ptm-80) REVERT: A 269 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.7647 (p90) REVERT: A 284 MET cc_start: 0.8769 (mtp) cc_final: 0.8511 (mtp) REVERT: A 476 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8055 (m-40) REVERT: A 616 ILE cc_start: 0.8382 (mp) cc_final: 0.8144 (mm) REVERT: A 631 LYS cc_start: 0.8605 (pttt) cc_final: 0.8353 (ptpt) REVERT: A 869 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7907 (tp) REVERT: A 919 MET cc_start: 0.9030 (tmm) cc_final: 0.8571 (ttt) REVERT: A 1007 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: A 1146 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: A 1157 PHE cc_start: 0.8591 (m-80) cc_final: 0.8183 (m-80) REVERT: C 57 ARG cc_start: 0.7957 (ptm-80) cc_final: 0.7507 (ptm160) REVERT: C 269 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8434 (p90) REVERT: C 346 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7494 (t0) REVERT: C 364 TYR cc_start: 0.8900 (t80) cc_final: 0.8523 (t80) REVERT: C 400 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8786 (mp) REVERT: C 754 PHE cc_start: 0.7848 (m-10) cc_final: 0.7556 (m-10) REVERT: C 838 MET cc_start: 0.7603 (mmm) cc_final: 0.7378 (mmp) REVERT: C 952 MET cc_start: 0.8542 (tpp) cc_final: 0.8146 (tpp) REVERT: C 1146 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7539 (m-80) outliers start: 152 outliers final: 96 residues processed: 419 average time/residue: 0.1782 time to fit residues: 124.4356 Evaluate side-chains 376 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 266 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 968 GLU Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1174 SER Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1146 PHE Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 831 VAL Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 945 SER Chi-restraints excluded: chain C residue 998 VAL Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1041 VAL Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1146 PHE Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1159 THR Chi-restraints excluded: chain C residue 1174 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 163 optimal weight: 0.1980 chunk 189 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 chunk 342 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102680 restraints weight = 42077.369| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.17 r_work: 0.3029 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29229 Z= 0.157 Angle : 0.610 11.554 39858 Z= 0.306 Chirality : 0.046 0.312 4617 Planarity : 0.004 0.047 4995 Dihedral : 6.384 55.962 5785 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.53 % Favored : 94.21 % Rotamer: Outliers : 4.60 % Allowed : 24.00 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3453 helix: 0.14 (0.20), residues: 720 sheet: -0.18 (0.19), residues: 648 loop : -1.47 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 358 TYR 0.022 0.001 TYR C 194 PHE 0.019 0.001 PHE C 953 TRP 0.011 0.001 TRP C 293 HIS 0.008 0.001 HIS A1171 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (29082) covalent geometry : angle 0.59020 / 0.30 (39468) SS BOND : bond 0.00369 / 0.24 ( 51) SS BOND : angle 1.58988 / 1.17 ( 102) hydrogen bonds : bond 0.03520 / 2.34 ( 831) hydrogen bonds : angle 5.31151 / 3.61 ( 2289) link_BETA1-4 : bond 0.00511 / 0.30 ( 30) link_BETA1-4 : angle 1.75293 / 1.19 ( 90) link_NAG-ASN : bond 0.00234 / 0.16 ( 66) link_NAG-ASN : angle 1.69826 / 1.15 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 273 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TYR cc_start: 0.8678 (m-80) cc_final: 0.8374 (m-80) REVERT: B 167 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7522 (mt-10) REVERT: B 172 VAL cc_start: 0.9034 (t) cc_final: 0.8622 (p) REVERT: B 400 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8772 (mp) REVERT: B 803 PHE cc_start: 0.8191 (t80) cc_final: 0.7742 (t80) REVERT: B 1175 ARG cc_start: 0.7698 (tmm160) cc_final: 0.7356 (ptm-80) REVERT: A 269 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.7637 (p90) REVERT: A 284 MET cc_start: 0.8737 (mtp) cc_final: 0.8466 (mtp) REVERT: A 311 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8152 (t0) REVERT: A 476 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8101 (m-40) REVERT: A 616 ILE cc_start: 0.8375 (mp) cc_final: 0.8141 (mm) REVERT: A 690 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7299 (t80) REVERT: A 838 MET cc_start: 0.7540 (mmm) cc_final: 0.7169 (mmp) REVERT: A 869 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7942 (tp) REVERT: A 919 MET cc_start: 0.9020 (tmm) cc_final: 0.8560 (ttt) REVERT: A 1007 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: A 1146 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.6740 (m-80) REVERT: A 1157 PHE cc_start: 0.8533 (m-80) cc_final: 0.8123 (m-80) REVERT: C 47 ARG cc_start: 0.8300 (mtm110) cc_final: 0.8019 (mtm110) REVERT: C 57 ARG cc_start: 0.7953 (ptm-80) cc_final: 0.7512 (ptm160) REVERT: C 79 MET cc_start: 0.8766 (tmm) cc_final: 0.8540 (ppp) REVERT: C 194 TYR cc_start: 0.7888 (t80) cc_final: 0.7664 (t80) REVERT: C 269 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8320 (p90) REVERT: C 346 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7469 (t0) REVERT: C 364 TYR cc_start: 0.8915 (t80) cc_final: 0.8521 (t80) REVERT: C 400 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8765 (mp) REVERT: C 411 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: C 952 MET cc_start: 0.8558 (tpp) cc_final: 0.8142 (tpp) REVERT: C 1146 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: C 1175 ARG cc_start: 0.7669 (tmm160) cc_final: 0.7467 (tmm160) outliers start: 138 outliers final: 97 residues processed: 401 average time/residue: 0.1835 time to fit residues: 122.9923 Evaluate side-chains 376 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 266 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1174 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1072 SER Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1146 PHE Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 831 VAL Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 945 SER Chi-restraints excluded: chain C residue 998 VAL Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1041 VAL Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1146 PHE Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1174 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 288 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 147 optimal weight: 0.2980 chunk 196 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1171 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.104183 restraints weight = 41854.335| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.21 r_work: 0.3065 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29229 Z= 0.114 Angle : 0.585 12.290 39858 Z= 0.292 Chirality : 0.045 0.392 4617 Planarity : 0.003 0.046 4995 Dihedral : 6.123 56.056 5785 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.98 % Favored : 94.76 % Rotamer: Outliers : 4.13 % Allowed : 24.73 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.14), residues: 3453 helix: 0.22 (0.20), residues: 732 sheet: -0.06 (0.19), residues: 660 loop : -1.47 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 358 TYR 0.028 0.001 TYR B 194 PHE 0.017 0.001 PHE B 754 TRP 0.013 0.001 TRP C 293 HIS 0.008 0.001 HIS A1171 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (29082) covalent geometry : angle 0.56347 / 0.29 (39468) SS BOND : bond 0.00352 / 0.20 ( 51) SS BOND : angle 1.36812 / 1.00 ( 102) hydrogen bonds : bond 0.03142 / 2.09 ( 831) hydrogen bonds : angle 5.17598 / 3.51 ( 2289) link_BETA1-4 : bond 0.00479 / 0.29 ( 30) link_BETA1-4 : angle 1.68667 / 1.14 ( 90) link_NAG-ASN : bond 0.00251 / 0.18 ( 66) link_NAG-ASN : angle 1.79655 / 1.21 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 287 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TYR cc_start: 0.8665 (m-80) cc_final: 0.8367 (m-80) REVERT: B 172 VAL cc_start: 0.9033 (t) cc_final: 0.8626 (p) REVERT: B 239 ARG cc_start: 0.6087 (mpt180) cc_final: 0.5874 (mmt180) REVERT: B 400 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8826 (mp) REVERT: B 1042 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: B 1175 ARG cc_start: 0.7729 (tmm160) cc_final: 0.7449 (ptm-80) REVERT: A 183 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7596 (mtpp) REVERT: A 269 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.7583 (p90) REVERT: A 284 MET cc_start: 0.8679 (mtp) cc_final: 0.8433 (mtp) REVERT: A 400 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8777 (mp) REVERT: A 476 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8023 (m-40) REVERT: A 616 ILE cc_start: 0.8416 (mp) cc_final: 0.8180 (mm) REVERT: A 919 MET cc_start: 0.9088 (tmm) cc_final: 0.8532 (ttt) REVERT: A 1007 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: A 1044 ASP cc_start: 0.8259 (t70) cc_final: 0.7735 (t0) REVERT: A 1134 ASN cc_start: 0.8126 (t0) cc_final: 0.7726 (m-40) REVERT: A 1146 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.6673 (m-80) REVERT: A 1157 PHE cc_start: 0.8540 (m-80) cc_final: 0.8136 (m-80) REVERT: C 47 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8014 (mtm110) REVERT: C 57 ARG cc_start: 0.7922 (ptm-80) cc_final: 0.7668 (ptm160) REVERT: C 400 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8864 (mp) REVERT: C 439 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.7163 (t80) REVERT: C 516 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7289 (ttt180) REVERT: C 952 MET cc_start: 0.8644 (tpp) cc_final: 0.8174 (tpp) REVERT: C 1134 ASN cc_start: 0.8399 (t0) cc_final: 0.8030 (m-40) REVERT: C 1146 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: C 1175 ARG cc_start: 0.7770 (tmm160) cc_final: 0.7514 (tmm160) REVERT: C 1179 GLN cc_start: 0.8424 (pm20) cc_final: 0.8087 (pp30) outliers start: 124 outliers final: 84 residues processed: 397 average time/residue: 0.1676 time to fit residues: 109.7654 Evaluate side-chains 365 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 268 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1174 SER Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1146 PHE Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 831 VAL Chi-restraints excluded: chain C residue 903 GLN Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1041 VAL Chi-restraints excluded: chain C residue 1072 SER Chi-restraints excluded: chain C residue 1146 PHE Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1174 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 297 optimal weight: 6.9990 chunk 227 optimal weight: 0.1980 chunk 189 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 356 ASN A1171 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.106319 restraints weight = 41879.122| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.06 r_work: 0.3083 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29229 Z= 0.112 Angle : 0.571 11.599 39858 Z= 0.285 Chirality : 0.044 0.364 4617 Planarity : 0.003 0.046 4995 Dihedral : 5.906 56.029 5785 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.21 % Favored : 94.53 % Rotamer: Outliers : 4.40 % Allowed : 24.33 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.14), residues: 3453 helix: 0.17 (0.20), residues: 753 sheet: 0.01 (0.20), residues: 645 loop : -1.42 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 358 TYR 0.023 0.001 TYR B 194 PHE 0.022 0.001 PHE C 754 TRP 0.009 0.001 TRP C 293 HIS 0.009 0.001 HIS A1171 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (29082) covalent geometry : angle 0.55373 / 0.28 (39468) SS BOND : bond 0.00277 / 0.18 ( 51) SS BOND : angle 1.31120 / 0.95 ( 102) hydrogen bonds : bond 0.03042 / 2.02 ( 831) hydrogen bonds : angle 5.04521 / 3.41 ( 2289) link_BETA1-4 : bond 0.00488 / 0.29 ( 30) link_BETA1-4 : angle 1.60275 / 1.08 ( 90) link_NAG-ASN : bond 0.00230 / 0.16 ( 66) link_NAG-ASN : angle 1.59329 / 1.09 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 274 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 VAL cc_start: 0.9011 (t) cc_final: 0.8607 (p) REVERT: B 400 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8790 (mp) REVERT: B 653 ASN cc_start: 0.8645 (m-40) cc_final: 0.8329 (p0) REVERT: B 838 MET cc_start: 0.7723 (mmm) cc_final: 0.7372 (mmp) REVERT: B 1042 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: B 1175 ARG cc_start: 0.7842 (tmm160) cc_final: 0.7577 (ptm-80) REVERT: A 47 ARG cc_start: 0.8260 (mtm110) cc_final: 0.7997 (mtm110) REVERT: A 74 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7360 (tm-30) REVERT: A 239 ARG cc_start: 0.5904 (mmt180) cc_final: 0.5672 (mmt180) REVERT: A 269 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.7548 (p90) REVERT: A 284 MET cc_start: 0.8716 (mtp) cc_final: 0.8466 (mtp) REVERT: A 400 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8700 (tp) REVERT: A 476 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7988 (m-40) REVERT: A 616 ILE cc_start: 0.8319 (mp) cc_final: 0.8053 (mm) REVERT: A 653 ASN cc_start: 0.8702 (m-40) cc_final: 0.8459 (p0) REVERT: A 1007 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: A 1044 ASP cc_start: 0.8210 (t70) cc_final: 0.7687 (t0) REVERT: A 1134 ASN cc_start: 0.8133 (t0) cc_final: 0.7751 (m-40) REVERT: A 1146 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.6451 (m-80) REVERT: A 1157 PHE cc_start: 0.8533 (m-80) cc_final: 0.8149 (m-80) REVERT: A 1175 ARG cc_start: 0.7556 (tmm160) cc_final: 0.7300 (tmm160) REVERT: C 47 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7895 (mtm110) REVERT: C 400 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8816 (mp) REVERT: C 415 HIS cc_start: 0.7677 (m170) cc_final: 0.7067 (t70) REVERT: C 420 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7831 (mm-30) REVERT: C 516 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7135 (ttt180) REVERT: C 631 LYS cc_start: 0.8781 (ptpt) cc_final: 0.8489 (ptmt) REVERT: C 952 MET cc_start: 0.8614 (tpp) cc_final: 0.8138 (tpp) REVERT: C 1134 ASN cc_start: 0.8323 (t0) cc_final: 0.7961 (m-40) REVERT: C 1146 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7294 (m-80) REVERT: C 1154 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6821 (p0) REVERT: C 1175 ARG cc_start: 0.7750 (tmm160) cc_final: 0.7462 (tmm160) REVERT: C 1179 GLN cc_start: 0.8412 (pm20) cc_final: 0.8068 (pp30) outliers start: 132 outliers final: 92 residues processed: 393 average time/residue: 0.1795 time to fit residues: 116.7075 Evaluate side-chains 372 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 268 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1174 SER Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1146 PHE Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 831 VAL Chi-restraints excluded: chain C residue 914 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 945 SER Chi-restraints excluded: chain C residue 1041 VAL Chi-restraints excluded: chain C residue 1072 SER Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1146 PHE Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1174 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 317 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 157 optimal weight: 0.0030 chunk 302 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1171 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103602 restraints weight = 41805.482| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.10 r_work: 0.3038 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29229 Z= 0.168 Angle : 0.613 11.637 39858 Z= 0.307 Chirality : 0.046 0.380 4617 Planarity : 0.004 0.047 4995 Dihedral : 6.031 55.835 5785 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.76 % Favored : 94.01 % Rotamer: Outliers : 4.27 % Allowed : 24.57 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3453 helix: 0.04 (0.20), residues: 768 sheet: -0.02 (0.19), residues: 660 loop : -1.45 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 358 TYR 0.023 0.001 TYR B 194 PHE 0.022 0.001 PHE C 754 TRP 0.014 0.001 TRP C 293 HIS 0.009 0.001 HIS A1171 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (29082) covalent geometry : angle 0.59411 / 0.30 (39468) SS BOND : bond 0.00424 / 0.27 ( 51) SS BOND : angle 1.61919 / 1.17 ( 102) hydrogen bonds : bond 0.03517 / 2.34 ( 831) hydrogen bonds : angle 5.13947 / 3.47 ( 2289) link_BETA1-4 : bond 0.00484 / 0.28 ( 30) link_BETA1-4 : angle 1.56857 / 1.05 ( 90) link_NAG-ASN : bond 0.00228 / 0.16 ( 66) link_NAG-ASN : angle 1.69897 / 1.16 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 269 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 VAL cc_start: 0.8940 (t) cc_final: 0.8549 (p) REVERT: B 229 GLU cc_start: 0.8828 (tt0) cc_final: 0.8546 (tt0) REVERT: B 653 ASN cc_start: 0.8669 (m-40) cc_final: 0.8349 (p0) REVERT: B 1042 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: B 1175 ARG cc_start: 0.7795 (tmm160) cc_final: 0.7519 (ptm-80) REVERT: A 269 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7632 (p90) REVERT: A 284 MET cc_start: 0.8753 (mtp) cc_final: 0.8497 (mtp) REVERT: A 476 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8084 (m-40) REVERT: A 616 ILE cc_start: 0.8407 (mp) cc_final: 0.8162 (mm) REVERT: A 653 ASN cc_start: 0.8710 (m-40) cc_final: 0.8482 (p0) REVERT: A 919 MET cc_start: 0.8987 (tmm) cc_final: 0.8544 (ttt) REVERT: A 1007 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: A 1134 ASN cc_start: 0.8154 (t0) cc_final: 0.7780 (m-40) REVERT: A 1146 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.6650 (m-80) REVERT: A 1157 PHE cc_start: 0.8536 (m-80) cc_final: 0.8139 (m-80) REVERT: C 47 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7882 (mtm110) REVERT: C 239 ARG cc_start: 0.5998 (mmt180) cc_final: 0.5749 (mmt180) REVERT: C 269 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8436 (p90) REVERT: C 364 TYR cc_start: 0.8911 (t80) cc_final: 0.8520 (t80) REVERT: C 631 LYS cc_start: 0.8756 (ptpt) cc_final: 0.8459 (ptmt) REVERT: C 838 MET cc_start: 0.7705 (mmm) cc_final: 0.7396 (mmp) REVERT: C 919 MET cc_start: 0.8875 (tmm) cc_final: 0.8668 (ttt) REVERT: C 952 MET cc_start: 0.8654 (tpp) cc_final: 0.8184 (tpp) REVERT: C 1134 ASN cc_start: 0.8486 (t0) cc_final: 0.8061 (m-40) REVERT: C 1146 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: C 1154 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6803 (p0) REVERT: C 1175 ARG cc_start: 0.7757 (tmm160) cc_final: 0.7544 (tmm160) outliers start: 128 outliers final: 101 residues processed: 388 average time/residue: 0.1679 time to fit residues: 108.8050 Evaluate side-chains 375 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 265 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 945 SER Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1174 SER Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1146 PHE Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 831 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 945 SER Chi-restraints excluded: chain C residue 998 VAL Chi-restraints excluded: chain C residue 1041 VAL Chi-restraints excluded: chain C residue 1072 SER Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1146 PHE Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1174 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 224 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 266 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1171 HIS ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105269 restraints weight = 41690.392| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.07 r_work: 0.3057 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29229 Z= 0.132 Angle : 0.590 11.556 39858 Z= 0.294 Chirality : 0.045 0.348 4617 Planarity : 0.003 0.046 4995 Dihedral : 5.949 55.951 5785 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.36 % Favored : 94.44 % Rotamer: Outliers : 3.87 % Allowed : 25.10 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3453 helix: 0.08 (0.20), residues: 768 sheet: -0.01 (0.20), residues: 645 loop : -1.42 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 358 TYR 0.022 0.001 TYR B 194 PHE 0.022 0.001 PHE C 953 TRP 0.009 0.001 TRP C 293 HIS 0.010 0.001 HIS A1171 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (29082) covalent geometry : angle 0.57183 / 0.29 (39468) SS BOND : bond 0.00325 / 0.21 ( 51) SS BOND : angle 1.44636 / 1.05 ( 102) hydrogen bonds : bond 0.03211 / 2.13 ( 831) hydrogen bonds : angle 5.07090 / 3.43 ( 2289) link_BETA1-4 : bond 0.00487 / 0.29 ( 30) link_BETA1-4 : angle 1.55338 / 1.05 ( 90) link_NAG-ASN : bond 0.00246 / 0.17 ( 66) link_NAG-ASN : angle 1.61898 / 1.11 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 272 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 VAL cc_start: 0.8926 (t) cc_final: 0.8536 (p) REVERT: B 229 GLU cc_start: 0.8798 (tt0) cc_final: 0.8502 (tt0) REVERT: B 400 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8805 (mp) REVERT: B 653 ASN cc_start: 0.8644 (m-40) cc_final: 0.8358 (p0) REVERT: B 1042 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: B 1175 ARG cc_start: 0.7824 (tmm160) cc_final: 0.7556 (ptm-80) REVERT: A 269 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7543 (p90) REVERT: A 284 MET cc_start: 0.8727 (mtp) cc_final: 0.8464 (mtp) REVERT: A 400 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8733 (tp) REVERT: A 476 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.8060 (m-40) REVERT: A 616 ILE cc_start: 0.8384 (mp) cc_final: 0.8140 (mm) REVERT: A 653 ASN cc_start: 0.8677 (m-40) cc_final: 0.8473 (p0) REVERT: A 919 MET cc_start: 0.8990 (tmm) cc_final: 0.8510 (ttt) REVERT: A 1007 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: A 1044 ASP cc_start: 0.8239 (t70) cc_final: 0.7699 (t0) REVERT: A 1134 ASN cc_start: 0.8157 (t0) cc_final: 0.7792 (m-40) REVERT: A 1146 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: A 1157 PHE cc_start: 0.8520 (m-80) cc_final: 0.8160 (m-80) REVERT: A 1175 ARG cc_start: 0.7581 (tmm160) cc_final: 0.7365 (tmm160) REVERT: C 47 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7808 (mtm110) REVERT: C 239 ARG cc_start: 0.6004 (mmt180) cc_final: 0.5719 (mmt180) REVERT: C 269 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8443 (p90) REVERT: C 364 TYR cc_start: 0.8891 (t80) cc_final: 0.8487 (t80) REVERT: C 400 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8820 (mp) REVERT: C 415 HIS cc_start: 0.7687 (m170) cc_final: 0.7072 (t70) REVERT: C 420 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7821 (mm-30) REVERT: C 631 LYS cc_start: 0.8742 (ptpt) cc_final: 0.8442 (ptmt) REVERT: C 653 ASN cc_start: 0.8642 (m-40) cc_final: 0.8370 (p0) REVERT: C 838 MET cc_start: 0.7690 (mmm) cc_final: 0.7398 (mmp) REVERT: C 919 MET cc_start: 0.8891 (tmm) cc_final: 0.8668 (ttt) REVERT: C 952 MET cc_start: 0.8631 (tpp) cc_final: 0.8174 (tpp) REVERT: C 1134 ASN cc_start: 0.8466 (t0) cc_final: 0.8075 (m-40) REVERT: C 1146 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: C 1154 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6843 (p0) REVERT: C 1175 ARG cc_start: 0.7741 (tmm160) cc_final: 0.7494 (tmm160) REVERT: C 1179 GLN cc_start: 0.8349 (pm20) cc_final: 0.8123 (pp30) outliers start: 116 outliers final: 98 residues processed: 379 average time/residue: 0.1839 time to fit residues: 115.6502 Evaluate side-chains 375 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 265 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 312 TYR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 427 TYR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1019 THR Chi-restraints excluded: chain B residue 1041 VAL Chi-restraints excluded: chain B residue 1042 GLN Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1174 SER Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 607 CYS Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1087 SER Chi-restraints excluded: chain A residue 1146 PHE Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 690 PHE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 831 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 SER Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 945 SER Chi-restraints excluded: chain C residue 998 VAL Chi-restraints excluded: chain C residue 1041 VAL Chi-restraints excluded: chain C residue 1072 SER Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1146 PHE Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1174 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 22 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 167 optimal weight: 0.0770 chunk 186 optimal weight: 6.9990 chunk 232 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 81 optimal weight: 0.0270 chunk 226 optimal weight: 0.8980 chunk 301 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 HIS ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107316 restraints weight = 41728.459| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.05 r_work: 0.3088 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 29229 Z= 0.103 Angle : 0.565 11.618 39858 Z= 0.282 Chirality : 0.044 0.311 4617 Planarity : 0.003 0.045 4995 Dihedral : 5.738 56.140 5785 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.79 % Rotamer: Outliers : 3.33 % Allowed : 25.77 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3453 helix: 0.21 (0.20), residues: 768 sheet: 0.02 (0.20), residues: 657 loop : -1.40 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 358 TYR 0.022 0.001 TYR B 194 PHE 0.026 0.001 PHE C 754 TRP 0.012 0.001 TRP C 293 HIS 0.009 0.001 HIS A1171 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (29082) covalent geometry : angle 0.54953 / 0.28 (39468) SS BOND : bond 0.00282 / 0.17 ( 51) SS BOND : angle 1.23447 / 0.89 ( 102) hydrogen bonds : bond 0.02844 / 1.90 ( 831) hydrogen bonds : angle 4.95261 / 3.34 ( 2289) link_BETA1-4 : bond 0.00471 / 0.28 ( 30) link_BETA1-4 : angle 1.52283 / 1.03 ( 90) link_NAG-ASN : bond 0.00293 / 0.20 ( 66) link_NAG-ASN : angle 1.45382 / 1.00 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5717.92 seconds wall clock time: 99 minutes 22.65 seconds (5962.65 seconds total)