Starting phenix.real_space_refine on Sat Mar 7 01:58:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hlc_34872/03_2026/8hlc_34872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hlc_34872/03_2026/8hlc_34872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hlc_34872/03_2026/8hlc_34872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hlc_34872/03_2026/8hlc_34872.map" model { file = "/net/cci-nas-00/data/ceres_data/8hlc_34872/03_2026/8hlc_34872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hlc_34872/03_2026/8hlc_34872.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 162 5.16 5 C 23316 2.51 5 N 6015 2.21 5 O 7287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36780 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 8451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8451 Classifications: {'peptide': 1081} Link IDs: {'PTRANS': 52, 'TRANS': 1028} Chain breaks: 6 Chain: "B" Number of atoms: 8451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8451 Classifications: {'peptide': 1081} Link IDs: {'PTRANS': 52, 'TRANS': 1028} Chain breaks: 6 Chain: "C" Number of atoms: 8451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8451 Classifications: {'peptide': 1081} Link IDs: {'PTRANS': 52, 'TRANS': 1028} Chain breaks: 6 Chain: "H" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1708 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "L" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Chain: "I" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1708 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "M" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Chain: "J" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1708 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "N" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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: "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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 216 Unusual residues: {'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} 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: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 216 Unusual residues: {'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 8.71, per 1000 atoms: 0.24 Number of scatterers: 36780 At special positions: 0 Unit cell: (164.137, 166.311, 235.879, 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 162 16.00 O 7287 8.00 N 6015 7.00 C 23316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.47 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.48 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.49 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.43 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.48 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.49 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.25 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.48 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.49 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 209 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 153 " - pdb=" SG CYS I 209 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 153 " - pdb=" SG CYS J 209 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " 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 A1303 " - " NAG A1304 " " NAG A1307 " - " NAG A1308 " " NAG A1309 " - " NAG A1310 " " NAG B1302 " - " NAG B1303 " " NAG B1305 " - " NAG B1306 " " NAG B1309 " - " NAG B1310 " " NAG B1311 " - " NAG B1312 " " NAG B1313 " - " NAG B1314 " " NAG C1302 " - " NAG C1303 " " NAG C1305 " - " NAG C1306 " " NAG C1309 " - " NAG C1310 " " NAG C1311 " - " NAG C1312 " " NAG C1313 " - " NAG C1314 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " NAG U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " NAG c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 801 " " NAG B1311 " - " ASN B1074 " " NAG B1313 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 801 " " NAG C1311 " - " ASN C1074 " " NAG C1313 " - " ASN C1134 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 282 " " NAG O 1 " - " ASN A 331 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A1074 " " NAG S 1 " - " ASN A1098 " " NAG T 1 " - " ASN B 17 " " NAG U 1 " - " ASN B 122 " " NAG V 1 " - " ASN B 165 " " NAG W 1 " - " ASN B 234 " " NAG X 1 " - " ASN B 282 " " NAG Y 1 " - " ASN B 331 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN C 17 " " NAG c 1 " - " ASN C 122 " " NAG d 1 " - " ASN C 165 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 282 " " NAG g 1 " - " ASN C 331 " " NAG h 1 " - " ASN C 717 " " NAG i 1 " - " ASN C1098 " Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.5 seconds 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8490 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 78 sheets defined 18.9% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.622A pdb=" N SER A 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.868A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.682A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.682A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.503A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.745A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 841 removed outlier: 4.060A pdb=" N LEU A 841 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.099A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.477A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.621A pdb=" N SER B 151 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.543A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.682A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.683A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.502A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.743A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 841 removed outlier: 4.059A pdb=" N LEU B 841 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.099A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.476A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.620A pdb=" N SER C 151 " --> pdb=" O ASN C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 removed outlier: 3.660A pdb=" N SER C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.682A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.682A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.502A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.745A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 841 removed outlier: 4.060A pdb=" N LEU C 841 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.100A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.478A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.827A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 56 removed outlier: 4.034A pdb=" N SER H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.827A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 56 removed outlier: 4.033A pdb=" N SER I 56 " --> pdb=" O SER I 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 53 through 56' Processing helix chain 'I' and resid 200 through 202 No H-bonds generated for 'chain 'I' and resid 200 through 202' Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.828A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 56 removed outlier: 4.033A pdb=" N SER J 56 " --> pdb=" O SER J 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 53 through 56' Processing helix chain 'J' and resid 200 through 202 No H-bonds generated for 'chain 'J' and resid 200 through 202' Processing helix chain 'N' and resid 121 through 128 Processing helix chain 'N' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.590A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.853A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.233A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 11.097A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.416A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.355A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.243A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.232A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 11.097A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.006A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.153A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.490A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.963A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.576A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.576A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.589A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP B 64 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.788A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.234A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.142A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.416A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.356A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.243A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.142A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.008A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.153A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.491A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 7.123A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.590A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP C 64 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.924A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.233A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.415A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.355A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.243A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.654A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.006A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.152A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.490A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.626A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.780A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.576A pdb=" N ARG H 98 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 133 through 137 removed outlier: 5.007A pdb=" N ALA H 150 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 197 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 152 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL H 195 " --> pdb=" O GLY H 152 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 154 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 193 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS H 156 " --> pdb=" O LEU H 191 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 191 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 133 through 137 removed outlier: 5.007A pdb=" N ALA H 150 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 197 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 152 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL H 195 " --> pdb=" O GLY H 152 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 154 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 193 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS H 156 " --> pdb=" O LEU H 191 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 191 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 163 through 167 Processing sheet with id=AF7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'L' and resid 11 through 13 Processing sheet with id=AF9, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.472A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 114 through 118 Processing sheet with id=AG2, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AG3, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.626A pdb=" N SER I 71 " --> pdb=" O TYR I 80 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.780A pdb=" N MET I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.576A pdb=" N ARG I 98 " --> pdb=" O VAL I 115 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL I 115 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 133 through 137 removed outlier: 5.008A pdb=" N ALA I 150 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL I 197 " --> pdb=" O ALA I 150 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 152 " --> pdb=" O VAL I 195 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 195 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 154 " --> pdb=" O SER I 193 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 193 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 156 " --> pdb=" O LEU I 191 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU I 191 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 133 through 137 removed outlier: 5.008A pdb=" N ALA I 150 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL I 197 " --> pdb=" O ALA I 150 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 152 " --> pdb=" O VAL I 195 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 195 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 154 " --> pdb=" O SER I 193 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 193 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 156 " --> pdb=" O LEU I 191 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU I 191 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 163 through 167 Processing sheet with id=AG9, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'M' and resid 11 through 13 Processing sheet with id=AH2, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.472A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 114 through 118 Processing sheet with id=AH4, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AH5, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.626A pdb=" N SER J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.779A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.576A pdb=" N ARG J 98 " --> pdb=" O VAL J 115 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 133 through 137 removed outlier: 5.007A pdb=" N ALA J 150 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL J 197 " --> pdb=" O ALA J 150 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 152 " --> pdb=" O VAL J 195 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 195 " --> pdb=" O GLY J 152 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU J 154 " --> pdb=" O SER J 193 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 193 " --> pdb=" O LEU J 154 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS J 156 " --> pdb=" O LEU J 191 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 191 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 133 through 137 removed outlier: 5.007A pdb=" N ALA J 150 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL J 197 " --> pdb=" O ALA J 150 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 152 " --> pdb=" O VAL J 195 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 195 " --> pdb=" O GLY J 152 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU J 154 " --> pdb=" O SER J 193 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 193 " --> pdb=" O LEU J 154 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS J 156 " --> pdb=" O LEU J 191 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 191 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 163 through 167 Processing sheet with id=AI2, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AI3, first strand: chain 'N' and resid 11 through 13 Processing sheet with id=AI4, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.473A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'N' and resid 114 through 118 Processing sheet with id=AI6, first strand: chain 'N' and resid 153 through 154 1478 hydrogen bonds defined for protein. 3858 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: 11.20 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11520 1.34 - 1.47: 9812 1.47 - 1.59: 16060 1.59 - 1.72: 0 1.72 - 1.85: 204 Bond restraints: 37596 Sorted by residual: bond pdb=" C1 NAG P 2 " pdb=" C2 NAG P 2 " ideal model delta sigma weight residual 1.532 1.417 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C1 NAG B1303 " pdb=" C2 NAG B1303 " ideal model delta sigma weight residual 1.532 1.417 0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C1 NAG C1303 " pdb=" C2 NAG C1303 " ideal model delta sigma weight residual 1.532 1.417 0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.302 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.303 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 37591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 49892 2.63 - 5.26: 1053 5.26 - 7.88: 151 7.88 - 10.51: 24 10.51 - 13.14: 3 Bond angle restraints: 51123 Sorted by residual: angle pdb=" N ARG C 847 " pdb=" CA ARG C 847 " pdb=" C ARG C 847 " ideal model delta sigma weight residual 114.56 107.66 6.90 1.27e+00 6.20e-01 2.95e+01 angle pdb=" N ARG B 847 " pdb=" CA ARG B 847 " pdb=" C ARG B 847 " ideal model delta sigma weight residual 114.56 107.66 6.90 1.27e+00 6.20e-01 2.95e+01 angle pdb=" N ARG A 847 " pdb=" CA ARG A 847 " pdb=" C ARG A 847 " ideal model delta sigma weight residual 114.56 107.69 6.87 1.27e+00 6.20e-01 2.93e+01 angle pdb=" N LYS C 278 " pdb=" CA LYS C 278 " pdb=" C LYS C 278 " ideal model delta sigma weight residual 110.42 102.11 8.31 1.55e+00 4.16e-01 2.88e+01 angle pdb=" N LYS A 278 " pdb=" CA LYS A 278 " pdb=" C LYS A 278 " ideal model delta sigma weight residual 110.17 102.13 8.04 1.61e+00 3.86e-01 2.49e+01 ... (remaining 51118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 20559 17.54 - 35.08: 2034 35.08 - 52.62: 705 52.62 - 70.16: 238 70.16 - 87.70: 44 Dihedral angle restraints: 23580 sinusoidal: 10338 harmonic: 13242 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -3.09 -82.91 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.57 80.57 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.55 80.55 1 1.00e+01 1.00e-02 8.02e+01 ... (remaining 23577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.308: 5986 0.308 - 0.617: 17 0.617 - 0.925: 6 0.925 - 1.233: 12 1.233 - 1.542: 12 Chirality restraints: 6033 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" O4 NAG B1305 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.51e+03 chirality pdb=" C1 NAG A1304 " pdb=" O4 NAG A1303 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.49e+03 chirality pdb=" C1 NAG C1306 " pdb=" O4 NAG C1305 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.49e+03 ... (remaining 6030 not shown) Planarity restraints: 6516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " -0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN B 657 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " 0.578 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " -0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN A 657 " -0.103 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " 0.092 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.577 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " 0.197 2.00e-02 2.50e+03 3.29e-01 1.36e+03 pdb=" CG ASN C 657 " -0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " -0.576 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " 0.391 2.00e-02 2.50e+03 ... (remaining 6513 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 199 2.48 - 3.09: 24730 3.09 - 3.69: 51443 3.69 - 4.30: 80035 4.30 - 4.90: 135572 Nonbonded interactions: 291979 Sorted by model distance: nonbonded pdb=" O THR B 124 " pdb=" ND2 ASN B 125 " model vdw 1.878 3.120 nonbonded pdb=" O THR A 124 " pdb=" ND2 ASN A 125 " model vdw 1.878 3.120 nonbonded pdb=" O THR C 124 " pdb=" ND2 ASN C 125 " model vdw 1.879 3.120 nonbonded pdb=" O SER A 940 " pdb=" OG1 THR A 941 " model vdw 1.909 3.040 nonbonded pdb=" O SER C 940 " pdb=" OG1 THR C 941 " model vdw 1.911 3.040 ... (remaining 291974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1310) selection = (chain 'B' and resid 14 through 1310) selection = (chain 'C' and resid 14 through 1310) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'E' selection = chain 'U' selection = chain 'c' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 38.090 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.150 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 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 : 0.012 0.457 37746 Z= 0.565 Angle : 1.425 58.527 51516 Z= 0.654 Chirality : 0.104 1.542 6033 Planarity : 0.009 0.218 6465 Dihedral : 16.710 87.698 14919 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 1.40 % Allowed : 7.55 % Favored : 91.05 % Rotamer: Outliers : 9.44 % Allowed : 12.63 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.11), residues: 4515 helix: -0.95 (0.18), residues: 729 sheet: -0.42 (0.14), residues: 1170 loop : -2.83 (0.10), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 98 TYR 0.022 0.002 TYR B 756 PHE 0.024 0.002 PHE A 133 TRP 0.030 0.002 TRP I 101 HIS 0.007 0.002 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00825 (37596) covalent geometry : angle 0.95762 (51123) SS BOND : bond 0.16864 ( 57) SS BOND : angle 11.31570 ( 114) hydrogen bonds : bond 0.13937 ( 1379) hydrogen bonds : angle 7.21591 ( 3858) link_BETA1-4 : bond 0.15014 ( 42) link_BETA1-4 : angle 11.50932 ( 126) link_NAG-ASN : bond 0.06050 ( 51) link_NAG-ASN : angle 13.13545 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 373 poor density : 601 time to evaluate : 1.659 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: A 146 HIS cc_start: 0.2971 (OUTLIER) cc_final: 0.2559 (m170) REVERT: A 147 LYS cc_start: 0.2383 (OUTLIER) cc_final: 0.1805 (tptp) REVERT: A 164 ASN cc_start: 0.7399 (p0) cc_final: 0.7084 (p0) REVERT: A 269 TYR cc_start: 0.7679 (m-80) cc_final: 0.7477 (m-80) REVERT: A 271 GLN cc_start: 0.6910 (mt0) cc_final: 0.6584 (mp10) REVERT: A 333 THR cc_start: 0.7036 (OUTLIER) cc_final: 0.6794 (t) REVERT: A 366 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8682 (p) REVERT: A 503 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 505 TYR cc_start: 0.7802 (m-80) cc_final: 0.7148 (t80) REVERT: A 531 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.6994 (p) REVERT: A 571 ASP cc_start: 0.7203 (m-30) cc_final: 0.6997 (t70) REVERT: A 606 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.7158 (t0) REVERT: A 708 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8437 (t) REVERT: A 848 ASP cc_start: 0.7068 (t0) cc_final: 0.6634 (t0) REVERT: A 868 GLU cc_start: 0.7318 (mp0) cc_final: 0.7013 (mp0) REVERT: A 977 LEU cc_start: 0.8731 (mt) cc_final: 0.8416 (mt) REVERT: A 982 SER cc_start: 0.7590 (OUTLIER) cc_final: 0.7334 (p) REVERT: A 1019 ARG cc_start: 0.7829 (tpt170) cc_final: 0.7590 (ttm170) REVERT: B 52 GLN cc_start: 0.6815 (tm-30) cc_final: 0.6516 (tt0) REVERT: B 141 LEU cc_start: 0.6934 (tt) cc_final: 0.6727 (mp) REVERT: B 145 TYR cc_start: 0.0915 (OUTLIER) cc_final: 0.0159 (m-10) REVERT: B 155 SER cc_start: 0.4654 (OUTLIER) cc_final: 0.4202 (m) REVERT: B 224 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: B 278 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.6016 (ptmt) REVERT: B 345 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8180 (m) REVERT: B 366 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7828 (t) REVERT: B 503 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8392 (p) REVERT: B 516 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6848 (pt0) REVERT: B 558 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7542 (mmmt) REVERT: B 617 CYS cc_start: 0.6448 (OUTLIER) cc_final: 0.5872 (m) REVERT: B 636 TYR cc_start: 0.7509 (m-80) cc_final: 0.7295 (m-80) REVERT: B 746 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8188 (t) REVERT: B 869 MET cc_start: 0.8351 (mtt) cc_final: 0.8140 (mtt) REVERT: C 28 TYR cc_start: 0.6759 (m-80) cc_final: 0.6482 (m-80) REVERT: C 52 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7515 (tp40) REVERT: C 114 THR cc_start: 0.8080 (m) cc_final: 0.7657 (p) REVERT: C 224 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6544 (mt-10) REVERT: C 375 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8334 (p) REVERT: C 606 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8092 (m-40) REVERT: C 612 TYR cc_start: 0.8501 (m-80) cc_final: 0.8213 (m-80) REVERT: C 731 MET cc_start: 0.8852 (ptt) cc_final: 0.8493 (ptt) REVERT: C 740 MET cc_start: 0.8579 (ttt) cc_final: 0.8257 (ttm) REVERT: C 790 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7506 (ptmm) REVERT: C 823 PHE cc_start: 0.7275 (t80) cc_final: 0.7009 (t80) REVERT: C 979 ASP cc_start: 0.7512 (m-30) cc_final: 0.7288 (t70) REVERT: C 1017 GLU cc_start: 0.7712 (tt0) cc_final: 0.7485 (tt0) REVERT: C 1019 ARG cc_start: 0.7975 (tpt170) cc_final: 0.7543 (tmm-80) REVERT: C 1029 MET cc_start: 0.8759 (tpp) cc_final: 0.8211 (tpp) REVERT: C 1107 ARG cc_start: 0.8518 (mtt180) cc_final: 0.8122 (mtt180) REVERT: I 169 SER cc_start: 0.1003 (OUTLIER) cc_final: 0.0728 (p) REVERT: I 216 SER cc_start: 0.0815 (OUTLIER) cc_final: 0.0586 (t) REVERT: J 169 SER cc_start: -0.1447 (OUTLIER) cc_final: -0.1680 (p) REVERT: J 177 HIS cc_start: 0.3042 (OUTLIER) cc_final: 0.2574 (m170) REVERT: J 210 ASN cc_start: 0.1683 (OUTLIER) cc_final: 0.1060 (p0) REVERT: N 108 ARG cc_start: 0.2859 (OUTLIER) cc_final: 0.1402 (mmt-90) outliers start: 373 outliers final: 51 residues processed: 881 average time/residue: 0.5442 time to fit residues: 604.8878 Evaluate side-chains 409 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 328 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 177 HIS Chi-restraints excluded: chain J residue 192 SER Chi-restraints excluded: chain J residue 210 ASN Chi-restraints excluded: chain N residue 108 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.0770 chunk 424 optimal weight: 20.0000 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 125 ASN A 188 ASN A 271 GLN A 314 GLN A 317 ASN A 448 ASN A 450 ASN A 544 ASN A 564 GLN A 613 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 804 GLN A 919 ASN A 925 ASN A 955 ASN A1002 GLN A1010 GLN A1023 ASN A1036 GLN A1054 GLN A1064 HIS A1142 GLN B 69 HIS B 87 ASN B 125 ASN B 188 ASN B 314 GLN B 317 ASN B 448 ASN B 450 ASN B 498 GLN B 532 ASN B 544 ASN B 564 GLN B 613 GLN B 644 GLN B 751 ASN B 779 GLN B 919 ASN B 925 ASN B1023 ASN B1036 GLN B1054 GLN B1064 HIS C 69 HIS C 99 ASN C 125 ASN C 188 ASN C 207 HIS C 280 ASN C 314 GLN C 317 ASN C 360 ASN C 448 ASN C 450 ASN C 498 GLN C 544 ASN C 564 GLN C 613 GLN C 644 GLN C 751 ASN C 804 GLN C 919 ASN C 925 ASN C1010 GLN C1023 ASN C1036 GLN C1054 GLN C1064 HIS C1125 ASN H 77 ASN H 177 HIS H 184 GLN H 210 ASN L 6 GLN L 90 GLN L 92 ASN I 77 ASN I 177 HIS I 184 GLN M 6 GLN M 92 ASN J 77 ASN J 184 GLN N 6 GLN Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.209147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157191 restraints weight = 45081.665| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 6.39 r_work: 0.3326 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37746 Z= 0.169 Angle : 0.849 16.370 51516 Z= 0.397 Chirality : 0.052 0.547 6033 Planarity : 0.005 0.069 6465 Dihedral : 9.384 73.033 7035 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.36 % Favored : 93.13 % Rotamer: Outliers : 4.61 % Allowed : 16.88 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.78 (0.12), residues: 4515 helix: 0.21 (0.19), residues: 729 sheet: 0.04 (0.14), residues: 1215 loop : -2.35 (0.10), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 142 TYR 0.031 0.002 TYR H 33 PHE 0.019 0.002 PHE B 194 TRP 0.025 0.002 TRP B 152 HIS 0.010 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00371 (37596) covalent geometry : angle 0.77180 (51123) SS BOND : bond 0.00774 ( 57) SS BOND : angle 1.48655 ( 114) hydrogen bonds : bond 0.05167 ( 1379) hydrogen bonds : angle 5.55381 ( 3858) link_BETA1-4 : bond 0.01057 ( 42) link_BETA1-4 : angle 3.64332 ( 126) link_NAG-ASN : bond 0.00684 ( 51) link_NAG-ASN : angle 5.59902 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 344 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7858 (m110) cc_final: 0.7615 (m-40) REVERT: A 177 MET cc_start: 0.4650 (mmp) cc_final: 0.4283 (ptm) REVERT: A 346 ARG cc_start: 0.7368 (ptm-80) cc_final: 0.6922 (ttt-90) REVERT: A 378 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8816 (tttt) REVERT: A 505 TYR cc_start: 0.8265 (m-80) cc_final: 0.7820 (t80) REVERT: A 531 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7454 (p) REVERT: A 571 ASP cc_start: 0.7756 (m-30) cc_final: 0.7511 (t70) REVERT: A 977 LEU cc_start: 0.8886 (mt) cc_final: 0.8669 (mt) REVERT: B 127 VAL cc_start: 0.8010 (m) cc_final: 0.7744 (t) REVERT: B 141 LEU cc_start: 0.6919 (tt) cc_final: 0.6624 (mp) REVERT: B 147 LYS cc_start: 0.2192 (OUTLIER) cc_final: 0.1951 (ptmm) REVERT: B 216 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6759 (pt) REVERT: B 558 LYS cc_start: 0.8659 (mptt) cc_final: 0.8418 (mmmt) REVERT: B 567 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7719 (mtt90) REVERT: B 636 TYR cc_start: 0.7933 (m-80) cc_final: 0.7683 (m-10) REVERT: B 780 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: B 869 MET cc_start: 0.8653 (mtt) cc_final: 0.8450 (mtt) REVERT: B 916 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8307 (tt) REVERT: C 197 ILE cc_start: 0.7665 (mt) cc_final: 0.7300 (mt) REVERT: C 236 THR cc_start: 0.8328 (m) cc_final: 0.8066 (p) REVERT: C 612 TYR cc_start: 0.8903 (m-80) cc_final: 0.8584 (m-80) REVERT: C 731 MET cc_start: 0.9035 (ptt) cc_final: 0.8617 (ptm) REVERT: C 790 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7970 (ptmm) REVERT: C 1029 MET cc_start: 0.8445 (tpp) cc_final: 0.8060 (tpp) REVERT: H 34 MET cc_start: 0.6660 (tpp) cc_final: 0.6396 (tpp) REVERT: H 79 LEU cc_start: 0.5529 (tp) cc_final: 0.4943 (mm) REVERT: H 83 MET cc_start: 0.2034 (mtt) cc_final: 0.1016 (ttp) REVERT: J 177 HIS cc_start: 0.2960 (OUTLIER) cc_final: 0.2383 (m170) REVERT: J 210 ASN cc_start: 0.2350 (OUTLIER) cc_final: 0.1746 (p0) REVERT: N 74 THR cc_start: 0.4219 (m) cc_final: 0.4013 (t) outliers start: 182 outliers final: 58 residues processed: 489 average time/residue: 0.5852 time to fit residues: 358.3269 Evaluate side-chains 344 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 276 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 177 HIS Chi-restraints excluded: chain J residue 210 ASN Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 176 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 347 optimal weight: 30.0000 chunk 371 optimal weight: 20.0000 chunk 283 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 211 optimal weight: 0.9980 chunk 450 optimal weight: 6.9990 chunk 444 optimal weight: 40.0000 chunk 298 optimal weight: 10.0000 chunk 247 optimal weight: 0.0070 chunk 74 optimal weight: 0.0570 overall best weight: 0.9718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1002 GLN B 87 ASN B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 606 ASN B 779 GLN B1071 GLN B1113 GLN B1119 ASN C 14 GLN C 218 GLN C 487 ASN C 675 GLN C 804 GLN C1005 GLN C1010 GLN L 90 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.208638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.156897 restraints weight = 45156.875| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 7.30 r_work: 0.3310 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37746 Z= 0.125 Angle : 0.728 17.874 51516 Z= 0.342 Chirality : 0.049 0.674 6033 Planarity : 0.004 0.051 6465 Dihedral : 8.108 68.357 6936 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.11 % Favored : 93.60 % Rotamer: Outliers : 3.47 % Allowed : 18.35 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.12), residues: 4515 helix: 0.92 (0.20), residues: 729 sheet: 0.30 (0.14), residues: 1251 loop : -2.11 (0.11), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.024 0.001 TYR H 33 PHE 0.025 0.001 PHE B 817 TRP 0.017 0.001 TRP H 101 HIS 0.008 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00263 (37596) covalent geometry : angle 0.66421 (51123) SS BOND : bond 0.00664 ( 57) SS BOND : angle 1.42244 ( 114) hydrogen bonds : bond 0.04395 ( 1379) hydrogen bonds : angle 5.23172 ( 3858) link_BETA1-4 : bond 0.00979 ( 42) link_BETA1-4 : angle 3.27763 ( 126) link_NAG-ASN : bond 0.00665 ( 51) link_NAG-ASN : angle 4.56923 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 295 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7532 (mm) REVERT: A 177 MET cc_start: 0.4758 (mmp) cc_final: 0.4365 (ptm) REVERT: A 378 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8780 (tttt) REVERT: A 505 TYR cc_start: 0.8250 (m-80) cc_final: 0.7681 (t80) REVERT: A 531 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7633 (p) REVERT: A 571 ASP cc_start: 0.7827 (m-30) cc_final: 0.7473 (t70) REVERT: A 977 LEU cc_start: 0.8809 (mt) cc_final: 0.8590 (mt) REVERT: B 127 VAL cc_start: 0.7823 (m) cc_final: 0.7566 (t) REVERT: B 216 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6650 (pt) REVERT: B 558 LYS cc_start: 0.8778 (mptt) cc_final: 0.8423 (mmmt) REVERT: B 567 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7661 (mtt90) REVERT: B 636 TYR cc_start: 0.7860 (m-80) cc_final: 0.7636 (m-10) REVERT: B 916 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8480 (tt) REVERT: B 1019 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8304 (tpt170) REVERT: C 197 ILE cc_start: 0.7802 (mt) cc_final: 0.7379 (mt) REVERT: C 277 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8276 (mt) REVERT: C 471 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6500 (mp0) REVERT: C 528 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7838 (mttm) REVERT: C 612 TYR cc_start: 0.8980 (m-80) cc_final: 0.8570 (m-80) REVERT: C 773 GLU cc_start: 0.8267 (tt0) cc_final: 0.7905 (tt0) REVERT: C 790 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7861 (ptmm) REVERT: C 1029 MET cc_start: 0.8471 (tpp) cc_final: 0.8233 (tpp) REVERT: H 79 LEU cc_start: 0.5516 (tp) cc_final: 0.5017 (mm) REVERT: H 98 ARG cc_start: 0.5511 (tmm160) cc_final: 0.5239 (tmm160) REVERT: I 5 VAL cc_start: 0.3889 (OUTLIER) cc_final: 0.3633 (t) REVERT: I 83 MET cc_start: 0.3823 (OUTLIER) cc_final: 0.3551 (mmm) REVERT: M 15 VAL cc_start: 0.4831 (OUTLIER) cc_final: 0.4448 (t) REVERT: J 177 HIS cc_start: 0.2708 (OUTLIER) cc_final: 0.2318 (m170) REVERT: J 210 ASN cc_start: 0.2045 (OUTLIER) cc_final: 0.1693 (p0) outliers start: 137 outliers final: 55 residues processed: 404 average time/residue: 0.5704 time to fit residues: 289.4030 Evaluate side-chains 320 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 252 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 177 HIS Chi-restraints excluded: chain J residue 192 SER Chi-restraints excluded: chain J residue 210 ASN Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 185 optimal weight: 10.0000 chunk 254 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 311 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 353 optimal weight: 30.0000 chunk 222 optimal weight: 0.8980 chunk 318 optimal weight: 0.5980 chunk 180 optimal weight: 0.5980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 271 GLN A 641 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN A1142 GLN B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 779 GLN B1125 ASN C 14 GLN C 188 ASN C 613 GLN C1005 GLN L 90 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.205670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.163293 restraints weight = 44848.003| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.72 r_work: 0.3467 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 37746 Z= 0.145 Angle : 0.734 15.806 51516 Z= 0.347 Chirality : 0.049 0.483 6033 Planarity : 0.004 0.053 6465 Dihedral : 7.681 61.198 6920 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.31 % Favored : 93.47 % Rotamer: Outliers : 3.92 % Allowed : 18.58 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.12), residues: 4515 helix: 0.87 (0.19), residues: 765 sheet: 0.47 (0.14), residues: 1245 loop : -2.00 (0.11), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.021 0.002 TYR H 33 PHE 0.020 0.002 PHE B 817 TRP 0.015 0.001 TRP H 101 HIS 0.007 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00331 (37596) covalent geometry : angle 0.67886 (51123) SS BOND : bond 0.00551 ( 57) SS BOND : angle 1.69927 ( 114) hydrogen bonds : bond 0.04707 ( 1379) hydrogen bonds : angle 5.21155 ( 3858) link_BETA1-4 : bond 0.00905 ( 42) link_BETA1-4 : angle 3.06674 ( 126) link_NAG-ASN : bond 0.00643 ( 51) link_NAG-ASN : angle 4.18151 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 291 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5030 (mmp) cc_final: 0.4646 (ptm) REVERT: A 378 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8841 (tttt) REVERT: A 505 TYR cc_start: 0.8104 (m-80) cc_final: 0.7837 (t80) REVERT: B 51 THR cc_start: 0.7199 (t) cc_final: 0.6865 (t) REVERT: B 153 MET cc_start: 0.2524 (tpt) cc_final: 0.0433 (mtp) REVERT: B 177 MET cc_start: 0.5477 (mmt) cc_final: 0.5263 (mmp) REVERT: B 216 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6644 (pt) REVERT: B 240 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8059 (m) REVERT: B 567 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7737 (mtt90) REVERT: B 636 TYR cc_start: 0.7991 (m-80) cc_final: 0.7579 (m-80) REVERT: B 916 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8591 (tt) REVERT: B 1019 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8151 (tpt170) REVERT: C 99 ASN cc_start: 0.7178 (m-40) cc_final: 0.6823 (m-40) REVERT: C 177 MET cc_start: 0.4501 (mmt) cc_final: 0.3470 (mmt) REVERT: C 197 ILE cc_start: 0.8221 (mt) cc_final: 0.7728 (mt) REVERT: C 277 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8495 (mt) REVERT: C 471 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6535 (mp0) REVERT: C 528 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7978 (mttm) REVERT: C 1005 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7376 (tm130) REVERT: C 1029 MET cc_start: 0.8376 (tpp) cc_final: 0.8112 (tpp) REVERT: H 79 LEU cc_start: 0.5610 (tp) cc_final: 0.5169 (mm) REVERT: I 5 VAL cc_start: 0.3911 (OUTLIER) cc_final: 0.3428 (t) REVERT: M 15 VAL cc_start: 0.5284 (OUTLIER) cc_final: 0.4783 (t) REVERT: J 128 SER cc_start: 0.3562 (p) cc_final: 0.3238 (m) REVERT: J 177 HIS cc_start: 0.2293 (OUTLIER) cc_final: 0.2039 (m170) REVERT: J 210 ASN cc_start: 0.1673 (OUTLIER) cc_final: 0.1412 (p0) outliers start: 155 outliers final: 69 residues processed: 412 average time/residue: 0.5741 time to fit residues: 297.7558 Evaluate side-chains 347 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 266 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 177 HIS Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 210 ASN Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 371 optimal weight: 7.9990 chunk 386 optimal weight: 30.0000 chunk 309 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 0.0010 chunk 446 optimal weight: 2.9990 chunk 325 optimal weight: 8.9990 chunk 380 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 779 GLN B1119 ASN B1142 GLN C 14 GLN C 188 ASN C 218 GLN L 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.202827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.158917 restraints weight = 44514.727| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.71 r_work: 0.3422 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 37746 Z= 0.173 Angle : 0.767 15.359 51516 Z= 0.364 Chirality : 0.051 0.802 6033 Planarity : 0.005 0.052 6465 Dihedral : 7.728 59.827 6916 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.56 % Favored : 93.22 % Rotamer: Outliers : 4.00 % Allowed : 18.45 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.04 (0.12), residues: 4515 helix: 0.77 (0.19), residues: 774 sheet: 0.60 (0.14), residues: 1269 loop : -1.99 (0.11), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 466 TYR 0.021 0.002 TYR J 33 PHE 0.022 0.002 PHE A 133 TRP 0.014 0.001 TRP C 353 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00406 (37596) covalent geometry : angle 0.70846 (51123) SS BOND : bond 0.00566 ( 57) SS BOND : angle 1.92454 ( 114) hydrogen bonds : bond 0.05216 ( 1379) hydrogen bonds : angle 5.31834 ( 3858) link_BETA1-4 : bond 0.00885 ( 42) link_BETA1-4 : angle 3.03448 ( 126) link_NAG-ASN : bond 0.00615 ( 51) link_NAG-ASN : angle 4.47430 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 281 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5125 (mmp) cc_final: 0.4726 (ptm) REVERT: A 378 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8840 (tttt) REVERT: A 505 TYR cc_start: 0.8116 (m-80) cc_final: 0.7819 (t80) REVERT: B 51 THR cc_start: 0.7146 (t) cc_final: 0.6855 (t) REVERT: B 153 MET cc_start: 0.2314 (tpt) cc_final: 0.0251 (mtp) REVERT: B 216 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6493 (pt) REVERT: B 240 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8148 (m) REVERT: B 394 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7875 (m-40) REVERT: B 567 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7806 (mtt90) REVERT: B 636 TYR cc_start: 0.7976 (m-80) cc_final: 0.7613 (m-80) REVERT: B 661 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: B 726 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9148 (mm) REVERT: B 916 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8754 (tp) REVERT: B 1019 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8097 (tpt170) REVERT: C 14 GLN cc_start: 0.5935 (OUTLIER) cc_final: 0.5687 (pm20) REVERT: C 99 ASN cc_start: 0.7225 (m-40) cc_final: 0.6917 (m-40) REVERT: C 177 MET cc_start: 0.4581 (mmt) cc_final: 0.3483 (mmt) REVERT: C 197 ILE cc_start: 0.8306 (mt) cc_final: 0.7771 (mt) REVERT: C 277 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8584 (mt) REVERT: C 465 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: C 471 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6776 (mp0) REVERT: C 900 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8587 (mmm) REVERT: C 1029 MET cc_start: 0.8325 (tpp) cc_final: 0.7990 (tpp) REVERT: H 34 MET cc_start: 0.6834 (tpp) cc_final: 0.5431 (mpp) REVERT: H 79 LEU cc_start: 0.5683 (tp) cc_final: 0.5209 (mm) REVERT: L 107 LYS cc_start: 0.3521 (OUTLIER) cc_final: 0.3190 (mtpp) REVERT: I 5 VAL cc_start: 0.4169 (OUTLIER) cc_final: 0.3755 (t) REVERT: I 103 LEU cc_start: 0.5448 (OUTLIER) cc_final: 0.4885 (mt) REVERT: M 15 VAL cc_start: 0.5181 (OUTLIER) cc_final: 0.4558 (t) REVERT: J 177 HIS cc_start: 0.2392 (OUTLIER) cc_final: 0.2067 (m170) REVERT: J 210 ASN cc_start: 0.1651 (OUTLIER) cc_final: 0.1352 (p0) outliers start: 158 outliers final: 76 residues processed: 406 average time/residue: 0.5883 time to fit residues: 297.8999 Evaluate side-chains 347 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 252 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 177 HIS Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 210 ASN Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 51 optimal weight: 6.9990 chunk 120 optimal weight: 0.0570 chunk 301 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 359 optimal weight: 50.0000 chunk 178 optimal weight: 0.8980 chunk 360 optimal weight: 7.9990 chunk 436 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 356 optimal weight: 7.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN A 271 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B 955 ASN L 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.204594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.153355 restraints weight = 44695.625| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 7.59 r_work: 0.3247 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 37746 Z= 0.124 Angle : 0.714 21.685 51516 Z= 0.338 Chirality : 0.051 1.232 6033 Planarity : 0.004 0.052 6465 Dihedral : 7.754 101.823 6915 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.91 % Favored : 93.86 % Rotamer: Outliers : 3.39 % Allowed : 19.31 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.12), residues: 4515 helix: 1.09 (0.19), residues: 765 sheet: 0.72 (0.14), residues: 1263 loop : -1.90 (0.11), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.028 0.001 TYR J 33 PHE 0.017 0.001 PHE A 133 TRP 0.010 0.001 TRP L 148 HIS 0.008 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00274 (37596) covalent geometry : angle 0.65396 (51123) SS BOND : bond 0.00448 ( 57) SS BOND : angle 2.05184 ( 114) hydrogen bonds : bond 0.04394 ( 1379) hydrogen bonds : angle 5.13702 ( 3858) link_BETA1-4 : bond 0.00857 ( 42) link_BETA1-4 : angle 2.85102 ( 126) link_NAG-ASN : bond 0.00655 ( 51) link_NAG-ASN : angle 4.33130 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 272 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5094 (mmp) cc_final: 0.4628 (ptm) REVERT: A 221 SER cc_start: 0.7651 (OUTLIER) cc_final: 0.7352 (t) REVERT: A 505 TYR cc_start: 0.8184 (m-80) cc_final: 0.7639 (t80) REVERT: A 558 LYS cc_start: 0.8350 (ttmm) cc_final: 0.8000 (mtmm) REVERT: B 51 THR cc_start: 0.7065 (t) cc_final: 0.6819 (t) REVERT: B 153 MET cc_start: 0.3327 (tpt) cc_final: 0.1552 (tpp) REVERT: B 177 MET cc_start: 0.4829 (mmt) cc_final: 0.4566 (mmp) REVERT: B 216 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6541 (mp) REVERT: B 286 THR cc_start: 0.8295 (m) cc_final: 0.8031 (p) REVERT: B 567 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7687 (mtt90) REVERT: B 726 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9159 (mm) REVERT: B 780 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: B 900 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8699 (mtm) REVERT: B 916 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8803 (tp) REVERT: B 983 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7607 (ptm160) REVERT: B 1019 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8354 (tpt170) REVERT: C 52 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7433 (tp40) REVERT: C 99 ASN cc_start: 0.7444 (m-40) cc_final: 0.7081 (m-40) REVERT: C 177 MET cc_start: 0.4403 (mmt) cc_final: 0.3482 (mmt) REVERT: C 197 ILE cc_start: 0.8146 (mt) cc_final: 0.7708 (mt) REVERT: C 202 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8325 (mptp) REVERT: C 277 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8582 (mt) REVERT: C 394 ASN cc_start: 0.8168 (t0) cc_final: 0.7968 (m-40) REVERT: C 773 GLU cc_start: 0.8516 (tt0) cc_final: 0.8229 (tt0) REVERT: C 957 GLN cc_start: 0.8715 (tt0) cc_final: 0.8511 (tp40) REVERT: C 979 ASP cc_start: 0.7958 (t70) cc_final: 0.7714 (t0) REVERT: C 1029 MET cc_start: 0.8482 (tpp) cc_final: 0.8172 (tpp) REVERT: H 34 MET cc_start: 0.6595 (tpp) cc_final: 0.5052 (mpp) REVERT: H 79 LEU cc_start: 0.5343 (tp) cc_final: 0.5030 (mm) REVERT: L 107 LYS cc_start: 0.2973 (OUTLIER) cc_final: 0.2611 (mtpt) REVERT: I 208 ILE cc_start: 0.1764 (OUTLIER) cc_final: 0.1448 (tp) REVERT: M 15 VAL cc_start: 0.4217 (OUTLIER) cc_final: 0.3739 (t) REVERT: J 34 MET cc_start: 0.4059 (tpt) cc_final: 0.3783 (tpp) REVERT: J 60 TYR cc_start: 0.3853 (m-80) cc_final: 0.3356 (m-80) REVERT: J 177 HIS cc_start: 0.2495 (OUTLIER) cc_final: 0.2060 (m170) REVERT: J 210 ASN cc_start: 0.1697 (OUTLIER) cc_final: 0.1333 (p0) outliers start: 134 outliers final: 64 residues processed: 380 average time/residue: 0.5871 time to fit residues: 278.0687 Evaluate side-chains 326 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 245 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 177 HIS Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 210 ASN Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 323 optimal weight: 0.9980 chunk 243 optimal weight: 0.9980 chunk 386 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 331 optimal weight: 0.5980 chunk 74 optimal weight: 0.0060 chunk 412 optimal weight: 20.0000 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN A1142 GLN B 87 ASN B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 613 GLN C 764 ASN L 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.206267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.166186 restraints weight = 44749.278| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.58 r_work: 0.3492 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 37746 Z= 0.113 Angle : 0.670 13.991 51516 Z= 0.318 Chirality : 0.048 0.785 6033 Planarity : 0.004 0.052 6465 Dihedral : 7.029 59.380 6914 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.96 % Favored : 93.84 % Rotamer: Outliers : 3.04 % Allowed : 19.84 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.12), residues: 4515 helix: 1.47 (0.20), residues: 747 sheet: 0.87 (0.14), residues: 1251 loop : -1.76 (0.11), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.023 0.001 TYR J 33 PHE 0.018 0.001 PHE B 133 TRP 0.019 0.001 TRP L 148 HIS 0.009 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00236 (37596) covalent geometry : angle 0.62525 (51123) SS BOND : bond 0.00403 ( 57) SS BOND : angle 1.71190 ( 114) hydrogen bonds : bond 0.03884 ( 1379) hydrogen bonds : angle 4.97488 ( 3858) link_BETA1-4 : bond 0.00924 ( 42) link_BETA1-4 : angle 2.69858 ( 126) link_NAG-ASN : bond 0.01023 ( 51) link_NAG-ASN : angle 3.49741 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 264 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 SER cc_start: 0.7600 (OUTLIER) cc_final: 0.7371 (t) REVERT: A 324 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7322 (mt-10) REVERT: A 505 TYR cc_start: 0.8198 (m-80) cc_final: 0.7819 (t80) REVERT: A 558 LYS cc_start: 0.8299 (ttmm) cc_final: 0.8027 (mtmm) REVERT: A 708 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8660 (t) REVERT: B 51 THR cc_start: 0.7289 (t) cc_final: 0.7013 (t) REVERT: B 153 MET cc_start: 0.2445 (tpt) cc_final: 0.0871 (tpt) REVERT: B 177 MET cc_start: 0.5185 (mmt) cc_final: 0.4873 (mmp) REVERT: B 216 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6605 (mp) REVERT: B 224 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8399 (mt-10) REVERT: B 661 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: B 726 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9117 (mm) REVERT: B 916 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8806 (tp) REVERT: B 1019 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8401 (tpt170) REVERT: C 52 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7540 (tp40) REVERT: C 197 ILE cc_start: 0.8091 (mt) cc_final: 0.7779 (mt) REVERT: C 471 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: C 773 GLU cc_start: 0.8528 (tt0) cc_final: 0.8225 (tt0) REVERT: C 979 ASP cc_start: 0.8084 (t70) cc_final: 0.7864 (t0) REVERT: C 1029 MET cc_start: 0.8376 (tpp) cc_final: 0.8165 (tpp) REVERT: H 79 LEU cc_start: 0.5580 (tp) cc_final: 0.5234 (mm) REVERT: L 107 LYS cc_start: 0.3330 (OUTLIER) cc_final: 0.2749 (mtpt) REVERT: M 9 PHE cc_start: 0.4497 (OUTLIER) cc_final: 0.4051 (t80) REVERT: J 34 MET cc_start: 0.5330 (tpt) cc_final: 0.4902 (tpp) REVERT: J 177 HIS cc_start: 0.2250 (OUTLIER) cc_final: 0.1835 (m170) REVERT: J 210 ASN cc_start: 0.1646 (OUTLIER) cc_final: 0.1284 (p0) outliers start: 120 outliers final: 53 residues processed: 356 average time/residue: 0.6400 time to fit residues: 285.0428 Evaluate side-chains 309 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 242 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 177 HIS Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 210 ASN Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 74 optimal weight: 0.5980 chunk 366 optimal weight: 0.9990 chunk 420 optimal weight: 8.9990 chunk 448 optimal weight: 7.9990 chunk 292 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 434 optimal weight: 7.9990 chunk 210 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 52 GLN B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 779 GLN C 14 GLN C 99 ASN L 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.200747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.149325 restraints weight = 43990.756| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 5.68 r_work: 0.3118 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 37746 Z= 0.210 Angle : 0.797 14.943 51516 Z= 0.384 Chirality : 0.052 0.597 6033 Planarity : 0.005 0.051 6465 Dihedral : 7.456 59.861 6910 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.64 % Favored : 93.18 % Rotamer: Outliers : 3.37 % Allowed : 19.84 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.12), residues: 4515 helix: 0.79 (0.19), residues: 780 sheet: 0.75 (0.14), residues: 1257 loop : -1.90 (0.11), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1000 TYR 0.023 0.002 TYR J 33 PHE 0.025 0.002 PHE A 133 TRP 0.012 0.002 TRP C 353 HIS 0.007 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00510 (37596) covalent geometry : angle 0.74745 (51123) SS BOND : bond 0.00644 ( 57) SS BOND : angle 2.73743 ( 114) hydrogen bonds : bond 0.05784 ( 1379) hydrogen bonds : angle 5.43486 ( 3858) link_BETA1-4 : bond 0.00788 ( 42) link_BETA1-4 : angle 2.90992 ( 126) link_NAG-ASN : bond 0.00593 ( 51) link_NAG-ASN : angle 3.79548 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 260 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4887 (mmp) cc_final: 0.4356 (ptm) REVERT: A 221 SER cc_start: 0.7742 (OUTLIER) cc_final: 0.7471 (t) REVERT: A 324 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 505 TYR cc_start: 0.8349 (m-80) cc_final: 0.7763 (t80) REVERT: A 708 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8715 (t) REVERT: A 811 LYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6471 (mttp) REVERT: B 51 THR cc_start: 0.7499 (t) cc_final: 0.7174 (t) REVERT: B 153 MET cc_start: 0.2297 (tpt) cc_final: 0.0512 (tpt) REVERT: B 177 MET cc_start: 0.4788 (mmt) cc_final: 0.4450 (mmp) REVERT: B 216 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6733 (mp) REVERT: B 567 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7884 (mtt90) REVERT: B 661 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: B 726 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9220 (mm) REVERT: B 916 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8772 (tp) REVERT: B 1019 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8626 (tpt170) REVERT: C 111 ASP cc_start: 0.8492 (t0) cc_final: 0.8287 (t0) REVERT: C 202 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7748 (mptp) REVERT: C 471 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: C 1029 MET cc_start: 0.8553 (tpp) cc_final: 0.8177 (tpp) REVERT: H 79 LEU cc_start: 0.5430 (tp) cc_final: 0.5106 (mm) REVERT: L 107 LYS cc_start: 0.3420 (OUTLIER) cc_final: 0.2906 (mtpt) REVERT: I 83 MET cc_start: 0.3653 (OUTLIER) cc_final: 0.3311 (mmp) REVERT: I 208 ILE cc_start: 0.1631 (OUTLIER) cc_final: 0.1322 (tp) REVERT: M 4 MET cc_start: 0.5817 (mmp) cc_final: 0.4165 (mmm) REVERT: M 9 PHE cc_start: 0.4240 (OUTLIER) cc_final: 0.3853 (t80) REVERT: J 34 MET cc_start: 0.4927 (tpt) cc_final: 0.4498 (tpp) REVERT: J 177 HIS cc_start: 0.2502 (OUTLIER) cc_final: 0.1948 (m170) REVERT: J 210 ASN cc_start: 0.1600 (OUTLIER) cc_final: 0.1272 (p0) outliers start: 133 outliers final: 69 residues processed: 365 average time/residue: 0.6106 time to fit residues: 276.8554 Evaluate side-chains 335 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 249 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 177 HIS Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 210 ASN Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 438 optimal weight: 20.0000 chunk 224 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 384 optimal weight: 50.0000 chunk 103 optimal weight: 0.9990 chunk 330 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN A 271 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 99 ASN C 613 GLN L 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.202672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152393 restraints weight = 44389.153| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 5.48 r_work: 0.3147 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37746 Z= 0.140 Angle : 0.731 23.336 51516 Z= 0.348 Chirality : 0.050 0.699 6033 Planarity : 0.004 0.051 6465 Dihedral : 7.181 59.869 6908 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.11 % Favored : 93.75 % Rotamer: Outliers : 2.48 % Allowed : 20.75 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.12), residues: 4515 helix: 0.99 (0.19), residues: 777 sheet: 0.74 (0.14), residues: 1248 loop : -1.81 (0.11), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.023 0.001 TYR J 33 PHE 0.024 0.001 PHE A 133 TRP 0.010 0.001 TRP C 353 HIS 0.007 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00320 (37596) covalent geometry : angle 0.67515 (51123) SS BOND : bond 0.00556 ( 57) SS BOND : angle 2.25347 ( 114) hydrogen bonds : bond 0.04728 ( 1379) hydrogen bonds : angle 5.24145 ( 3858) link_BETA1-4 : bond 0.00842 ( 42) link_BETA1-4 : angle 2.75512 ( 126) link_NAG-ASN : bond 0.00571 ( 51) link_NAG-ASN : angle 4.19065 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 241 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5188 (mmp) cc_final: 0.4470 (ptm) REVERT: A 221 SER cc_start: 0.7737 (OUTLIER) cc_final: 0.7447 (t) REVERT: A 324 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7258 (mt-10) REVERT: A 505 TYR cc_start: 0.8351 (m-80) cc_final: 0.7729 (t80) REVERT: A 558 LYS cc_start: 0.8405 (ttmm) cc_final: 0.8016 (mtmm) REVERT: A 661 GLU cc_start: 0.7768 (mp0) cc_final: 0.7329 (mt-10) REVERT: A 811 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6654 (mttp) REVERT: B 51 THR cc_start: 0.7443 (t) cc_final: 0.7184 (t) REVERT: B 153 MET cc_start: 0.2522 (tpt) cc_final: 0.0756 (tpp) REVERT: B 177 MET cc_start: 0.4688 (mmt) cc_final: 0.4353 (mmp) REVERT: B 216 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6638 (mp) REVERT: B 240 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8260 (m) REVERT: B 340 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: B 567 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7863 (mtt90) REVERT: B 661 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: B 726 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9165 (mm) REVERT: B 916 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8807 (tp) REVERT: B 1019 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8548 (tpt170) REVERT: C 202 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8223 (mmtt) REVERT: C 465 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: C 471 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: C 773 GLU cc_start: 0.8646 (tt0) cc_final: 0.8301 (tt0) REVERT: C 979 ASP cc_start: 0.8341 (t70) cc_final: 0.8099 (t0) REVERT: C 1029 MET cc_start: 0.8538 (tpp) cc_final: 0.8211 (tpp) REVERT: H 79 LEU cc_start: 0.5406 (tp) cc_final: 0.5052 (mm) REVERT: L 107 LYS cc_start: 0.3325 (OUTLIER) cc_final: 0.2889 (mtpt) REVERT: I 83 MET cc_start: 0.3555 (OUTLIER) cc_final: 0.3307 (mmp) REVERT: I 208 ILE cc_start: 0.1639 (OUTLIER) cc_final: 0.1333 (tp) REVERT: M 4 MET cc_start: 0.5805 (mmp) cc_final: 0.4019 (mmm) REVERT: M 9 PHE cc_start: 0.4289 (OUTLIER) cc_final: 0.3911 (t80) REVERT: J 34 MET cc_start: 0.4715 (tpt) cc_final: 0.4338 (tpp) REVERT: J 45 LEU cc_start: 0.4386 (mt) cc_final: 0.4093 (tp) REVERT: J 177 HIS cc_start: 0.2621 (OUTLIER) cc_final: 0.2047 (m170) REVERT: J 210 ASN cc_start: 0.1715 (OUTLIER) cc_final: 0.1402 (p0) outliers start: 98 outliers final: 61 residues processed: 320 average time/residue: 0.6139 time to fit residues: 243.9970 Evaluate side-chains 313 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 233 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 177 HIS Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 210 ASN Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 328 optimal weight: 20.0000 chunk 238 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 418 optimal weight: 9.9990 chunk 316 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 424 optimal weight: 30.0000 chunk 202 optimal weight: 3.9990 chunk 336 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 391 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN A 271 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B 856 ASN C 14 GLN C 99 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 160 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.199054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156183 restraints weight = 44110.008| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.63 r_work: 0.3402 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 37746 Z= 0.247 Angle : 0.842 16.287 51516 Z= 0.408 Chirality : 0.055 0.705 6033 Planarity : 0.005 0.061 6465 Dihedral : 7.686 59.464 6908 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 2.71 % Allowed : 20.53 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -1.03 (0.12), residues: 4515 helix: 0.57 (0.19), residues: 783 sheet: 0.65 (0.14), residues: 1272 loop : -1.94 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1039 TYR 0.026 0.002 TYR J 33 PHE 0.030 0.002 PHE A 133 TRP 0.016 0.002 TRP C 258 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00607 (37596) covalent geometry : angle 0.79120 (51123) SS BOND : bond 0.00725 ( 57) SS BOND : angle 2.91560 ( 114) hydrogen bonds : bond 0.06125 ( 1379) hydrogen bonds : angle 5.57548 ( 3858) link_BETA1-4 : bond 0.00779 ( 42) link_BETA1-4 : angle 2.95207 ( 126) link_NAG-ASN : bond 0.00653 ( 51) link_NAG-ASN : angle 3.98779 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 262 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4845 (mmp) cc_final: 0.4519 (ptm) REVERT: A 324 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7071 (mt-10) REVERT: A 505 TYR cc_start: 0.8062 (m-80) cc_final: 0.7767 (t80) REVERT: A 558 LYS cc_start: 0.8280 (ttmm) cc_final: 0.7880 (mtmm) REVERT: B 51 THR cc_start: 0.7473 (t) cc_final: 0.7112 (t) REVERT: B 153 MET cc_start: 0.1593 (tpt) cc_final: 0.0078 (tpt) REVERT: B 177 MET cc_start: 0.5468 (mmt) cc_final: 0.5190 (mmp) REVERT: B 216 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6652 (pt) REVERT: B 567 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7778 (mtt90) REVERT: B 661 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: B 726 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9236 (mm) REVERT: B 916 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8862 (tp) REVERT: B 1019 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8563 (tpt170) REVERT: C 202 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7638 (mptp) REVERT: C 465 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: C 471 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: C 1029 MET cc_start: 0.8367 (tpp) cc_final: 0.7929 (tpp) REVERT: H 83 MET cc_start: 0.2511 (mmp) cc_final: 0.1872 (mmm) REVERT: L 107 LYS cc_start: 0.3660 (OUTLIER) cc_final: 0.3088 (mtpt) REVERT: I 83 MET cc_start: 0.4397 (OUTLIER) cc_final: 0.4083 (mmp) REVERT: M 4 MET cc_start: 0.5553 (mmp) cc_final: 0.4408 (mmm) REVERT: M 9 PHE cc_start: 0.4599 (OUTLIER) cc_final: 0.4011 (t80) REVERT: J 34 MET cc_start: 0.6027 (tpt) cc_final: 0.5574 (tpp) REVERT: J 177 HIS cc_start: 0.2521 (OUTLIER) cc_final: 0.1899 (m170) REVERT: N 89 LEU cc_start: 0.5014 (tp) cc_final: 0.4706 (tp) outliers start: 107 outliers final: 71 residues processed: 347 average time/residue: 0.5795 time to fit residues: 251.0274 Evaluate side-chains 332 residues out of total 3951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 248 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 177 HIS Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 166 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 238 optimal weight: 5.9990 chunk 306 optimal weight: 0.8980 chunk 381 optimal weight: 30.0000 chunk 164 optimal weight: 7.9990 chunk 282 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 368 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 182 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN A 271 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 14 GLN C 99 ASN C 188 ASN C 501 ASN L 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.202536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150889 restraints weight = 44096.492| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 7.66 r_work: 0.3224 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37746 Z= 0.127 Angle : 0.702 14.177 51516 Z= 0.337 Chirality : 0.049 0.682 6033 Planarity : 0.004 0.051 6465 Dihedral : 7.129 59.537 6906 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.74 % Favored : 94.13 % Rotamer: Outliers : 2.25 % Allowed : 21.01 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.12), residues: 4515 helix: 1.05 (0.19), residues: 771 sheet: 0.74 (0.14), residues: 1266 loop : -1.74 (0.11), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.022 0.001 TYR J 33 PHE 0.020 0.001 PHE A 133 TRP 0.011 0.001 TRP C 436 HIS 0.007 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00283 (37596) covalent geometry : angle 0.65666 (51123) SS BOND : bond 0.00433 ( 57) SS BOND : angle 2.01476 ( 114) hydrogen bonds : bond 0.04508 ( 1379) hydrogen bonds : angle 5.24151 ( 3858) link_BETA1-4 : bond 0.00854 ( 42) link_BETA1-4 : angle 2.68123 ( 126) link_NAG-ASN : bond 0.00642 ( 51) link_NAG-ASN : angle 3.61682 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13309.31 seconds wall clock time: 227 minutes 19.56 seconds (13639.56 seconds total)