Starting phenix.real_space_refine on Sat Feb 7 02:07:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kr9_62523/02_2026/9kr9_62523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kr9_62523/02_2026/9kr9_62523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kr9_62523/02_2026/9kr9_62523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kr9_62523/02_2026/9kr9_62523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kr9_62523/02_2026/9kr9_62523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kr9_62523/02_2026/9kr9_62523.map" } 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= 0.004 sd= 0.135 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 156 5.16 5 C 18234 2.51 5 N 4650 2.21 5 O 5811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28851 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 9193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9193 Classifications: {'peptide': 1184} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1126} Chain breaks: 1 Chain: "C" Number of atoms: 9193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9193 Classifications: {'peptide': 1184} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1126} Chain breaks: 1 Chain: "B" Number of atoms: 9193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9193 Classifications: {'peptide': 1184} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1126} Chain breaks: 1 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: 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: "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: "J" 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "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: 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: "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: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'NAG': 10, 'PLM': 1} 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: "C" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'NAG': 10, 'PLM': 1} 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: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'NAG': 10, 'PLM': 1} 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 Time building chain proxies: 7.07, per 1000 atoms: 0.25 Number of scatterers: 28851 At special positions: 0 Unit cell: (150.006, 153.267, 169.572, 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 156 16.00 O 5811 8.00 N 4650 7.00 C 18234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 357 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 445 " - pdb=" SG CYS A 583 " distance=2.04 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS A 601 " - pdb=" SG CYS A 652 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 648 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 710 " distance=2.04 Simple disulfide: pdb=" SG CYS A 724 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 825 " distance=2.04 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 814 " distance=2.04 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 922 " distance=2.04 Simple disulfide: pdb=" SG CYS A1103 " - pdb=" SG CYS A1114 " distance=2.02 Simple disulfide: pdb=" SG CYS A1153 " - pdb=" SG CYS A1161 " distance=2.04 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 193 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS C 347 " - pdb=" SG CYS C 357 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 445 " - pdb=" SG CYS C 583 " distance=2.04 Simple disulfide: pdb=" SG CYS C 511 " - pdb=" SG CYS C 532 " distance=2.03 Simple disulfide: pdb=" SG CYS C 601 " - pdb=" SG CYS C 652 " distance=2.03 Simple disulfide: pdb=" SG CYS C 618 " - pdb=" SG CYS C 648 " distance=2.04 Simple disulfide: pdb=" SG CYS C 677 " - pdb=" SG CYS C 710 " distance=2.04 Simple disulfide: pdb=" SG CYS C 724 " - pdb=" SG CYS C 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 825 " distance=2.04 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 814 " distance=2.04 Simple disulfide: pdb=" SG CYS C 909 " - pdb=" SG CYS C 922 " distance=2.04 Simple disulfide: pdb=" SG CYS C1103 " - pdb=" SG CYS C1114 " distance=2.02 Simple disulfide: pdb=" SG CYS C1153 " - pdb=" SG CYS C1161 " distance=2.04 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 357 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 445 " - pdb=" SG CYS B 583 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 652 " distance=2.03 Simple disulfide: pdb=" SG CYS B 618 " - pdb=" SG CYS B 648 " distance=2.04 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 710 " distance=2.04 Simple disulfide: pdb=" SG CYS B 724 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 825 " distance=2.04 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 814 " distance=2.04 Simple disulfide: pdb=" SG CYS B 909 " - pdb=" SG CYS B 922 " distance=2.04 Simple disulfide: pdb=" SG CYS B1103 " - pdb=" SG CYS B1114 " distance=2.02 Simple disulfide: pdb=" SG CYS B1153 " - pdb=" SG CYS B1161 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " NAG P 3 " " 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " NAG Y 3 " " 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 d 1 " - " NAG d 2 " NAG-ASN " NAG A3002 " - " ASN A 73 " " NAG A3003 " - " ASN A 111 " " NAG A3004 " - " ASN A 132 " " NAG A3005 " - " ASN A 167 " " NAG A3006 " - " ASN A 244 " " NAG A3007 " - " ASN A 495 " " NAG A3008 " - " ASN A 590 " " NAG A3009 " - " ASN A 617 " " NAG A3010 " - " ASN A 716 " " NAG A3011 " - " ASN A 771 " " NAG B3002 " - " ASN B 73 " " NAG B3003 " - " ASN B 111 " " NAG B3004 " - " ASN B 132 " " NAG B3005 " - " ASN B 167 " " NAG B3006 " - " ASN B 244 " " NAG B3007 " - " ASN B 495 " " NAG B3008 " - " ASN B 590 " " NAG B3009 " - " ASN B 617 " " NAG B3010 " - " ASN B 716 " " NAG B3011 " - " ASN B 771 " " NAG C3002 " - " ASN C 73 " " NAG C3003 " - " ASN C 111 " " NAG C3004 " - " ASN C 132 " " NAG C3005 " - " ASN C 167 " " NAG C3006 " - " ASN C 244 " " NAG C3007 " - " ASN C 495 " " NAG C3008 " - " ASN C 590 " " NAG C3009 " - " ASN C 617 " " NAG C3010 " - " ASN C 716 " " NAG C3011 " - " ASN C 771 " " NAG D 1 " - " ASN A 174 " " NAG E 1 " - " ASN A 250 " " NAG F 1 " - " ASN A 418 " " NAG G 1 " - " ASN A 760 " " NAG H 1 " - " ASN A 782 " " NAG I 1 " - " ASN A 867 " " NAG J 1 " - " ASN A1145 " " NAG K 1 " - " ASN A1172 " " NAG L 1 " - " ASN A1214 " " NAG M 1 " - " ASN C 174 " " NAG N 1 " - " ASN C 250 " " NAG O 1 " - " ASN C 418 " " NAG P 1 " - " ASN C 760 " " NAG Q 1 " - " ASN C 782 " " NAG R 1 " - " ASN C 867 " " NAG S 1 " - " ASN C1145 " " NAG T 1 " - " ASN C1172 " " NAG U 1 " - " ASN C1214 " " NAG V 1 " - " ASN B 174 " " NAG W 1 " - " ASN B 250 " " NAG X 1 " - " ASN B 418 " " NAG Y 1 " - " ASN B 760 " " NAG Z 1 " - " ASN B 782 " " NAG a 1 " - " ASN B 867 " " NAG b 1 " - " ASN B1145 " " NAG c 1 " - " ASN B1172 " " NAG d 1 " - " ASN B1214 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.4 seconds 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6660 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 60 sheets defined 23.8% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 230 through 239 removed outlier: 3.802A pdb=" N TYR A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 315 removed outlier: 3.985A pdb=" N ARG A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.513A pdb=" N PHE A 407 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.643A pdb=" N LEU A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.734A pdb=" N ALA A 442 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.724A pdb=" N LEU A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 476 removed outlier: 4.011A pdb=" N GLN A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.793A pdb=" N THR A 693 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 698 " --> pdb=" O ASN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 808 Processing helix chain 'A' and resid 811 through 818 removed outlier: 3.609A pdb=" N LEU A 817 " --> pdb=" O LYS A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 822 removed outlier: 3.599A pdb=" N GLY A 822 " --> pdb=" O LYS A 819 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 819 through 822' Processing helix chain 'A' and resid 823 through 847 removed outlier: 3.786A pdb=" N LYS A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 838 " --> pdb=" O GLY A 834 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP A 840 " --> pdb=" O ASN A 836 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 845 " --> pdb=" O GLU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 885 through 893 removed outlier: 3.710A pdb=" N ASN A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 912 removed outlier: 3.656A pdb=" N CYS A 909 " --> pdb=" O GLY A 905 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET A 910 " --> pdb=" O TYR A 906 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 912 " --> pdb=" O GLU A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing helix chain 'A' and resid 940 through 950 removed outlier: 3.668A pdb=" N THR A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 950 " --> pdb=" O SER A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 978 removed outlier: 3.752A pdb=" N PHE A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 990 removed outlier: 3.747A pdb=" N GLU A 989 " --> pdb=" O GLN A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1003 removed outlier: 3.882A pdb=" N ALA A1001 " --> pdb=" O LYS A 997 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1002 " --> pdb=" O PHE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.668A pdb=" N THR A1007 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1035 removed outlier: 3.744A pdb=" N GLN A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1023 " --> pdb=" O VAL A1019 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A1030 " --> pdb=" O ASN A1026 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A1033 " --> pdb=" O ALA A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1038 No H-bonds generated for 'chain 'A' and resid 1036 through 1038' Processing helix chain 'A' and resid 1047 through 1055 removed outlier: 3.710A pdb=" N ALA A1053 " --> pdb=" O SER A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1103 removed outlier: 3.959A pdb=" N GLU A1061 " --> pdb=" O THR A1057 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A1062 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A1063 " --> pdb=" O GLU A1059 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A1065 " --> pdb=" O GLU A1061 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1067 " --> pdb=" O GLN A1063 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A1084 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A1094 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A1097 " --> pdb=" O ALA A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1224 removed outlier: 3.583A pdb=" N LEU A1224 " --> pdb=" O PRO A1221 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 230 through 239 removed outlier: 3.801A pdb=" N TYR C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 removed outlier: 3.986A pdb=" N ARG C 315 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 360 Processing helix chain 'C' and resid 393 through 397 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.513A pdb=" N PHE C 407 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 424 removed outlier: 3.643A pdb=" N LEU C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.734A pdb=" N ALA C 442 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 464 removed outlier: 3.724A pdb=" N LEU C 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 476 removed outlier: 4.011A pdb=" N GLN C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 698 removed outlier: 3.793A pdb=" N THR C 693 " --> pdb=" O ARG C 689 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG C 698 " --> pdb=" O ASN C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 808 Processing helix chain 'C' and resid 811 through 818 removed outlier: 3.609A pdb=" N LEU C 817 " --> pdb=" O LYS C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 822 removed outlier: 3.597A pdb=" N GLY C 822 " --> pdb=" O LYS C 819 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 819 through 822' Processing helix chain 'C' and resid 823 through 847 removed outlier: 3.786A pdb=" N LYS C 827 " --> pdb=" O GLN C 823 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 838 " --> pdb=" O GLY C 834 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP C 840 " --> pdb=" O ASN C 836 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 842 " --> pdb=" O ARG C 838 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 843 " --> pdb=" O GLN C 839 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 845 " --> pdb=" O GLU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 850 No H-bonds generated for 'chain 'C' and resid 848 through 850' Processing helix chain 'C' and resid 885 through 893 removed outlier: 3.709A pdb=" N ASN C 893 " --> pdb=" O ASP C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 912 removed outlier: 3.656A pdb=" N CYS C 909 " --> pdb=" O GLY C 905 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET C 910 " --> pdb=" O TYR C 906 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C 912 " --> pdb=" O GLU C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 928 Processing helix chain 'C' and resid 940 through 950 removed outlier: 3.669A pdb=" N THR C 945 " --> pdb=" O GLU C 941 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY C 950 " --> pdb=" O SER C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 978 removed outlier: 3.752A pdb=" N PHE C 974 " --> pdb=" O ALA C 970 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 990 removed outlier: 3.748A pdb=" N GLU C 989 " --> pdb=" O GLN C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1003 removed outlier: 3.882A pdb=" N ALA C1001 " --> pdb=" O LYS C 997 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C1002 " --> pdb=" O PHE C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1008 removed outlier: 3.668A pdb=" N THR C1007 " --> pdb=" O ALA C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1035 removed outlier: 3.745A pdb=" N GLN C1020 " --> pdb=" O PHE C1016 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C1022 " --> pdb=" O LYS C1018 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C1023 " --> pdb=" O VAL C1019 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU C1030 " --> pdb=" O ASN C1026 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C1033 " --> pdb=" O ALA C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1038 No H-bonds generated for 'chain 'C' and resid 1036 through 1038' Processing helix chain 'C' and resid 1047 through 1055 removed outlier: 3.710A pdb=" N ALA C1053 " --> pdb=" O SER C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1103 removed outlier: 3.958A pdb=" N GLU C1061 " --> pdb=" O THR C1057 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA C1062 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN C1063 " --> pdb=" O GLU C1059 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C1065 " --> pdb=" O GLU C1061 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG C1066 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C1067 " --> pdb=" O GLN C1063 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C1073 " --> pdb=" O ASN C1069 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C1074 " --> pdb=" O GLY C1070 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C1084 " --> pdb=" O ALA C1080 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN C1094 " --> pdb=" O ALA C1090 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C1097 " --> pdb=" O ALA C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1224 removed outlier: 3.583A pdb=" N LEU C1224 " --> pdb=" O PRO C1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 230 through 239 removed outlier: 3.803A pdb=" N TYR B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 315 removed outlier: 3.985A pdb=" N ARG B 315 " --> pdb=" O PHE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 360 Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.512A pdb=" N PHE B 407 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 424 removed outlier: 3.643A pdb=" N LEU B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.734A pdb=" N ALA B 442 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 removed outlier: 3.724A pdb=" N LEU B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 476 removed outlier: 4.011A pdb=" N GLN B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 removed outlier: 3.793A pdb=" N THR B 693 " --> pdb=" O ARG B 689 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 808 Processing helix chain 'B' and resid 811 through 818 removed outlier: 3.609A pdb=" N LEU B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 822 removed outlier: 3.598A pdb=" N GLY B 822 " --> pdb=" O LYS B 819 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 819 through 822' Processing helix chain 'B' and resid 823 through 847 removed outlier: 3.786A pdb=" N LYS B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 838 " --> pdb=" O GLY B 834 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 842 " --> pdb=" O ARG B 838 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 845 " --> pdb=" O GLU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 885 through 893 removed outlier: 3.709A pdb=" N ASN B 893 " --> pdb=" O ASP B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 912 removed outlier: 3.656A pdb=" N CYS B 909 " --> pdb=" O GLY B 905 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET B 910 " --> pdb=" O TYR B 906 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 912 " --> pdb=" O GLU B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 928 Processing helix chain 'B' and resid 940 through 950 removed outlier: 3.670A pdb=" N THR B 945 " --> pdb=" O GLU B 941 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 950 " --> pdb=" O SER B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 978 removed outlier: 3.752A pdb=" N PHE B 974 " --> pdb=" O ALA B 970 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 990 removed outlier: 3.748A pdb=" N GLU B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1003 removed outlier: 3.882A pdb=" N ALA B1001 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B1002 " --> pdb=" O PHE B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.669A pdb=" N THR B1007 " --> pdb=" O ALA B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1035 removed outlier: 3.745A pdb=" N GLN B1020 " --> pdb=" O PHE B1016 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B1022 " --> pdb=" O LYS B1018 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B1023 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B1030 " --> pdb=" O ASN B1026 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B1033 " --> pdb=" O ALA B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1038 No H-bonds generated for 'chain 'B' and resid 1036 through 1038' Processing helix chain 'B' and resid 1047 through 1055 removed outlier: 3.709A pdb=" N ALA B1053 " --> pdb=" O SER B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1103 removed outlier: 3.958A pdb=" N GLU B1061 " --> pdb=" O THR B1057 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA B1062 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B1063 " --> pdb=" O GLU B1059 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B1065 " --> pdb=" O GLU B1061 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG B1066 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B1067 " --> pdb=" O GLN B1063 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B1074 " --> pdb=" O GLY B1070 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B1084 " --> pdb=" O ALA B1080 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B1094 " --> pdb=" O ALA B1090 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B1097 " --> pdb=" O ALA B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1224 removed outlier: 3.582A pdb=" N LEU B1224 " --> pdb=" O PRO B1221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 82 removed outlier: 3.512A pdb=" N ILE A 74 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR A 330 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP A 346 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 332 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A 344 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN A 334 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.195A pdb=" N VAL A 271 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR A 291 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 273 " --> pdb=" O PHE A 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96 removed outlier: 7.228A pdb=" N SER A 95 " --> pdb=" O ILE A 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA6, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA7, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA8, first strand: chain 'A' and resid 134 through 137 removed outlier: 9.602A pdb=" N GLY A 135 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N SER A 142 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 137 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 317 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AB1, first strand: chain 'A' and resid 367 through 370 Processing sheet with id=AB2, first strand: chain 'A' and resid 380 through 384 removed outlier: 6.358A pdb=" N GLY A 380 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N SER A 605 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE A 382 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR A 646 " --> pdb=" O CYS A 618 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL A 637 " --> pdb=" O VAL A 649 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.436A pdb=" N GLN A 389 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N CYS A 415 " --> pdb=" O CYS A 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 408 through 412 removed outlier: 3.864A pdb=" N SER A 448 " --> pdb=" O GLN A 574 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 565 " --> pdb=" O VAL A 492 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A 485 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N CYS A 433 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG A 487 " --> pdb=" O PHE A 431 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 431 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 489 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.340A pdb=" N THR A 555 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS A 511 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR A 553 " --> pdb=" O CYS A 511 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 545 " --> pdb=" O GLY A 556 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 716 through 721 removed outlier: 6.151A pdb=" N ILE A 756 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N MET A 719 " --> pdb=" O ILE A 756 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1118 through 1127 removed outlier: 6.275A pdb=" N HIS A1119 " --> pdb=" O TYR A1138 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR A1138 " --> pdb=" O HIS A1119 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR A1147 " --> pdb=" O LEU A1171 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE A1169 " --> pdb=" O ALA A1149 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY A1189 " --> pdb=" O HIS A1194 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS A1194 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1118 through 1127 removed outlier: 6.275A pdb=" N HIS A1119 " --> pdb=" O TYR A1138 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR A1138 " --> pdb=" O HIS A1119 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY A1130 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU A 793 " --> pdb=" O GLY A1130 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR A1132 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE A 791 " --> pdb=" O TYR A1132 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE A1134 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN A 789 " --> pdb=" O PHE A1134 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A1136 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 787 " --> pdb=" O VAL A1136 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR A1138 " --> pdb=" O PHE A 785 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE A 785 " --> pdb=" O TYR A1138 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE A 783 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER A1142 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 775 " --> pdb=" O ALA A1148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 799 through 801 Processing sheet with id=AC1, first strand: chain 'A' and resid 862 through 863 Processing sheet with id=AC2, first strand: chain 'A' and resid 964 through 965 removed outlier: 3.510A pdb=" N PHE B 775 " --> pdb=" O ALA B1148 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER B1142 " --> pdb=" O THR B 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE B 783 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE B 785 " --> pdb=" O TYR B1138 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR B1138 " --> pdb=" O PHE B 785 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 787 " --> pdb=" O VAL B1136 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B1136 " --> pdb=" O VAL B 787 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLN B 789 " --> pdb=" O PHE B1134 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE B1134 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE B 791 " --> pdb=" O TYR B1132 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR B1132 " --> pdb=" O PHE B 791 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU B 793 " --> pdb=" O GLY B1130 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY B1130 " --> pdb=" O GLU B 793 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR B1138 " --> pdb=" O HIS B1119 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N HIS B1119 " --> pdb=" O TYR B1138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 964 through 965 removed outlier: 3.510A pdb=" N PHE B 775 " --> pdb=" O ALA B1148 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER B1142 " --> pdb=" O THR B 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE B 783 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE B 785 " --> pdb=" O TYR B1138 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR B1138 " --> pdb=" O PHE B 785 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 787 " --> pdb=" O VAL B1136 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B1136 " --> pdb=" O VAL B 787 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLN B 789 " --> pdb=" O PHE B1134 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE B1134 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE B 791 " --> pdb=" O TYR B1132 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR B1132 " --> pdb=" O PHE B 791 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU B 793 " --> pdb=" O GLY B1130 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY B1130 " --> pdb=" O GLU B 793 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR B1147 " --> pdb=" O LEU B1171 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B1169 " --> pdb=" O ALA B1149 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY B1189 " --> pdb=" O HIS B1194 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS B1194 " --> pdb=" O GLY B1189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1203 through 1205 Processing sheet with id=AC5, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AC6, first strand: chain 'C' and resid 74 through 82 removed outlier: 3.513A pdb=" N ILE C 74 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR C 330 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP C 346 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 332 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA C 344 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN C 334 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.196A pdb=" N VAL C 271 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR C 291 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU C 273 " --> pdb=" O PHE C 289 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 95 through 96 removed outlier: 7.228A pdb=" N SER C 95 " --> pdb=" O ILE C 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AD1, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AD2, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AD3, first strand: chain 'C' and resid 134 through 137 removed outlier: 9.602A pdb=" N GLY C 135 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N SER C 142 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR C 137 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 317 " --> pdb=" O PRO C 146 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AD5, first strand: chain 'C' and resid 367 through 370 Processing sheet with id=AD6, first strand: chain 'C' and resid 380 through 384 removed outlier: 6.358A pdb=" N GLY C 380 " --> pdb=" O GLU C 603 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N SER C 605 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE C 382 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR C 646 " --> pdb=" O CYS C 618 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL C 637 " --> pdb=" O VAL C 649 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 389 through 390 removed outlier: 6.436A pdb=" N GLN C 389 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N CYS C 415 " --> pdb=" O CYS C 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 408 through 412 removed outlier: 3.864A pdb=" N SER C 448 " --> pdb=" O GLN C 574 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C 565 " --> pdb=" O VAL C 492 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR C 485 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N CYS C 433 " --> pdb=" O THR C 485 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG C 487 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE C 431 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 489 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 519 through 521 removed outlier: 6.339A pdb=" N THR C 555 " --> pdb=" O THR C 509 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS C 511 " --> pdb=" O THR C 553 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR C 553 " --> pdb=" O CYS C 511 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 545 " --> pdb=" O GLY C 556 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 716 through 721 removed outlier: 6.151A pdb=" N ILE C 756 " --> pdb=" O SER C 717 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N MET C 719 " --> pdb=" O ILE C 756 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 758 " --> pdb=" O MET C 719 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1118 through 1127 removed outlier: 6.275A pdb=" N HIS C1119 " --> pdb=" O TYR C1138 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR C1138 " --> pdb=" O HIS C1119 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR C1147 " --> pdb=" O LEU C1171 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE C1169 " --> pdb=" O ALA C1149 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY C1189 " --> pdb=" O HIS C1194 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS C1194 " --> pdb=" O GLY C1189 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1118 through 1127 removed outlier: 6.275A pdb=" N HIS C1119 " --> pdb=" O TYR C1138 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR C1138 " --> pdb=" O HIS C1119 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY C1130 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU C 793 " --> pdb=" O GLY C1130 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR C1132 " --> pdb=" O PHE C 791 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE C 791 " --> pdb=" O TYR C1132 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE C1134 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLN C 789 " --> pdb=" O PHE C1134 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C1136 " --> pdb=" O VAL C 787 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C 787 " --> pdb=" O VAL C1136 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR C1138 " --> pdb=" O PHE C 785 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE C 785 " --> pdb=" O TYR C1138 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE C 783 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER C1142 " --> pdb=" O THR C 781 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 775 " --> pdb=" O ALA C1148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 799 through 801 Processing sheet with id=AE5, first strand: chain 'C' and resid 862 through 863 Processing sheet with id=AE6, first strand: chain 'C' and resid 1203 through 1205 Processing sheet with id=AE7, first strand: chain 'B' and resid 37 through 39 Processing sheet with id=AE8, first strand: chain 'B' and resid 74 through 82 removed outlier: 3.513A pdb=" N ILE B 74 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR B 330 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP B 346 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU B 332 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA B 344 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN B 334 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.195A pdb=" N VAL B 271 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR B 291 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 273 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 95 through 96 removed outlier: 7.228A pdb=" N SER B 95 " --> pdb=" O ILE B 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AF3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AF4, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AF5, first strand: chain 'B' and resid 134 through 137 removed outlier: 9.602A pdb=" N GLY B 135 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N SER B 142 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 137 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA B 317 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AF7, first strand: chain 'B' and resid 367 through 370 Processing sheet with id=AF8, first strand: chain 'B' and resid 380 through 384 removed outlier: 6.358A pdb=" N GLY B 380 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N SER B 605 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE B 382 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR B 646 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL B 637 " --> pdb=" O VAL B 649 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 389 through 390 removed outlier: 6.437A pdb=" N GLN B 389 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS B 415 " --> pdb=" O CYS B 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'B' and resid 408 through 412 removed outlier: 3.864A pdb=" N SER B 448 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 565 " --> pdb=" O VAL B 492 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR B 485 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N CYS B 433 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG B 487 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 431 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 489 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 519 through 521 removed outlier: 6.339A pdb=" N THR B 555 " --> pdb=" O THR B 509 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS B 511 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR B 553 " --> pdb=" O CYS B 511 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN B 545 " --> pdb=" O GLY B 556 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 716 through 721 removed outlier: 6.151A pdb=" N ILE B 756 " --> pdb=" O SER B 717 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N MET B 719 " --> pdb=" O ILE B 756 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 799 through 801 Processing sheet with id=AG5, first strand: chain 'B' and resid 862 through 863 Processing sheet with id=AG6, first strand: chain 'B' and resid 1203 through 1205 971 hydrogen bonds defined for protein. 2580 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: 7.16 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8984 1.34 - 1.46: 7509 1.46 - 1.58: 12805 1.58 - 1.70: 0 1.70 - 1.83: 210 Bond restraints: 29508 Sorted by residual: bond pdb=" C PRO C1221 " pdb=" N PRO C1222 " ideal model delta sigma weight residual 1.335 1.377 -0.043 1.19e-02 7.06e+03 1.29e+01 bond pdb=" C PRO A1221 " pdb=" N PRO A1222 " ideal model delta sigma weight residual 1.335 1.376 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" C PRO B1221 " pdb=" N PRO B1222 " ideal model delta sigma weight residual 1.335 1.376 -0.042 1.19e-02 7.06e+03 1.22e+01 bond pdb=" CA GLN A 823 " pdb=" CB GLN A 823 " ideal model delta sigma weight residual 1.523 1.489 0.035 1.27e-02 6.20e+03 7.46e+00 bond pdb=" CA GLN B 823 " pdb=" CB GLN B 823 " ideal model delta sigma weight residual 1.523 1.489 0.035 1.27e-02 6.20e+03 7.43e+00 ... (remaining 29503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 37842 1.91 - 3.83: 1993 3.83 - 5.74: 234 5.74 - 7.65: 92 7.65 - 9.57: 18 Bond angle restraints: 40179 Sorted by residual: angle pdb=" N MET C 396 " pdb=" CA MET C 396 " pdb=" C MET C 396 " ideal model delta sigma weight residual 114.75 107.28 7.47 1.26e+00 6.30e-01 3.51e+01 angle pdb=" N MET B 396 " pdb=" CA MET B 396 " pdb=" C MET B 396 " ideal model delta sigma weight residual 114.75 107.28 7.47 1.26e+00 6.30e-01 3.51e+01 angle pdb=" N MET A 396 " pdb=" CA MET A 396 " pdb=" C MET A 396 " ideal model delta sigma weight residual 114.75 107.29 7.46 1.26e+00 6.30e-01 3.51e+01 angle pdb=" N ALA A1001 " pdb=" CA ALA A1001 " pdb=" C ALA A1001 " ideal model delta sigma weight residual 114.56 107.13 7.43 1.27e+00 6.20e-01 3.42e+01 angle pdb=" N ALA C1001 " pdb=" CA ALA C1001 " pdb=" C ALA C1001 " ideal model delta sigma weight residual 114.56 107.16 7.40 1.27e+00 6.20e-01 3.40e+01 ... (remaining 40174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 16790 17.70 - 35.40: 1291 35.40 - 53.10: 438 53.10 - 70.80: 150 70.80 - 88.49: 57 Dihedral angle restraints: 18726 sinusoidal: 8319 harmonic: 10407 Sorted by residual: dihedral pdb=" CA GLY A 954 " pdb=" C GLY A 954 " pdb=" N ALA A 955 " pdb=" CA ALA A 955 " ideal model delta harmonic sigma weight residual 180.00 -144.13 -35.87 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" CA GLY C 954 " pdb=" C GLY C 954 " pdb=" N ALA C 955 " pdb=" CA ALA C 955 " ideal model delta harmonic sigma weight residual 180.00 -144.14 -35.86 0 5.00e+00 4.00e-02 5.14e+01 dihedral pdb=" CA GLY B 954 " pdb=" C GLY B 954 " pdb=" N ALA B 955 " pdb=" CA ALA B 955 " ideal model delta harmonic sigma weight residual -180.00 -144.19 -35.81 0 5.00e+00 4.00e-02 5.13e+01 ... (remaining 18723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4344 0.096 - 0.192: 420 0.192 - 0.288: 3 0.288 - 0.384: 3 0.384 - 0.480: 3 Chirality restraints: 4773 Sorted by residual: chirality pdb=" C1 NAG C3010 " pdb=" ND2 ASN C 716 " pdb=" C2 NAG C3010 " pdb=" O5 NAG C3010 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" C1 NAG A3010 " pdb=" ND2 ASN A 716 " pdb=" C2 NAG A3010 " pdb=" O5 NAG A3010 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" C1 NAG B3010 " pdb=" ND2 ASN B 716 " pdb=" C2 NAG B3010 " pdb=" O5 NAG B3010 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.63e+00 ... (remaining 4770 not shown) Planarity restraints: 5148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 PLM C3001 " -0.141 2.00e-02 2.50e+03 8.18e-02 6.68e+01 pdb=" C2 PLM C3001 " 0.040 2.00e-02 2.50e+03 pdb=" O1 PLM C3001 " 0.050 2.00e-02 2.50e+03 pdb=" O2 PLM C3001 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PLM A3001 " 0.141 2.00e-02 2.50e+03 8.17e-02 6.67e+01 pdb=" C2 PLM A3001 " -0.040 2.00e-02 2.50e+03 pdb=" O1 PLM A3001 " -0.050 2.00e-02 2.50e+03 pdb=" O2 PLM A3001 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PLM B3001 " 0.141 2.00e-02 2.50e+03 8.16e-02 6.66e+01 pdb=" C2 PLM B3001 " -0.040 2.00e-02 2.50e+03 pdb=" O1 PLM B3001 " -0.050 2.00e-02 2.50e+03 pdb=" O2 PLM B3001 " -0.051 2.00e-02 2.50e+03 ... (remaining 5145 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8407 2.81 - 3.33: 21962 3.33 - 3.85: 46055 3.85 - 4.38: 54797 4.38 - 4.90: 95978 Nonbonded interactions: 227199 Sorted by model distance: nonbonded pdb=" O PRO A 395 " pdb=" OH TYR A 453 " model vdw 2.286 3.040 nonbonded pdb=" O PRO B 395 " pdb=" OH TYR B 453 " model vdw 2.286 3.040 nonbonded pdb=" O PRO C 395 " pdb=" OH TYR C 453 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR C 559 " pdb=" O2 PLM C3001 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR A 559 " pdb=" O2 PLM A3001 " model vdw 2.288 3.040 ... (remaining 227194 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'G' selection = chain 'P' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.930 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 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 : 0.009 0.075 29646 Z= 0.402 Angle : 1.053 13.439 40542 Z= 0.595 Chirality : 0.057 0.480 4773 Planarity : 0.008 0.082 5091 Dihedral : 15.704 88.494 11913 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.98 % Rotamer: Outliers : 8.71 % Allowed : 9.07 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.27 % 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: -3.78 (0.11), residues: 3540 helix: -4.01 (0.11), residues: 759 sheet: -0.78 (0.18), residues: 768 loop : -2.68 (0.11), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 689 TYR 0.018 0.002 TYR B 192 PHE 0.022 0.003 PHE A 247 TRP 0.011 0.001 TRP B 957 HIS 0.005 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00894 (29508) covalent geometry : angle 0.99563 (40179) SS BOND : bond 0.00668 ( 51) SS BOND : angle 1.56540 ( 102) hydrogen bonds : bond 0.24516 ( 893) hydrogen bonds : angle 8.69595 ( 2580) link_BETA1-4 : bond 0.00657 ( 30) link_BETA1-4 : angle 2.87972 ( 90) link_NAG-ASN : bond 0.00795 ( 57) link_NAG-ASN : angle 4.90594 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 333 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: A 283 ARG cc_start: 0.5775 (mmm-85) cc_final: 0.5342 (mmm-85) REVERT: A 296 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: A 381 GLU cc_start: 0.7785 (tp30) cc_final: 0.7559 (tp30) REVERT: A 392 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6843 (t0) REVERT: A 397 LEU cc_start: 0.8633 (mt) cc_final: 0.8409 (mt) REVERT: A 517 TYR cc_start: 0.5177 (OUTLIER) cc_final: 0.4232 (p90) REVERT: A 552 LEU cc_start: 0.8251 (mp) cc_final: 0.7961 (mp) REVERT: A 557 TYR cc_start: 0.8260 (t80) cc_final: 0.8037 (t80) REVERT: A 586 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.5984 (mp10) REVERT: A 637 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8527 (m) REVERT: A 643 ASN cc_start: 0.7197 (OUTLIER) cc_final: 0.6941 (p0) REVERT: A 659 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8219 (t) REVERT: A 701 PRO cc_start: 0.5792 (Cg_exo) cc_final: 0.5465 (Cg_endo) REVERT: A 883 TYR cc_start: 0.8882 (p90) cc_final: 0.8641 (p90) REVERT: A 1006 GLN cc_start: 0.7168 (pt0) cc_final: 0.6868 (pp30) REVERT: A 1057 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8653 (m) REVERT: A 1059 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6669 (mm-30) REVERT: A 1061 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7201 (mt-10) REVERT: C 56 ASP cc_start: 0.7756 (t70) cc_final: 0.7188 (t0) REVERT: C 90 LYS cc_start: 0.7953 (tttt) cc_final: 0.7659 (tttp) REVERT: C 106 ASN cc_start: 0.4291 (OUTLIER) cc_final: 0.4068 (p0) REVERT: C 296 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: C 365 GLU cc_start: 0.6076 (mm-30) cc_final: 0.5681 (mp0) REVERT: C 390 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6887 (mt-10) REVERT: C 460 MET cc_start: 0.8049 (mtp) cc_final: 0.7196 (mtp) REVERT: C 517 TYR cc_start: 0.5176 (OUTLIER) cc_final: 0.3928 (p90) REVERT: C 586 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.5967 (mp10) REVERT: C 603 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7059 (tp30) REVERT: C 617 ASN cc_start: 0.6042 (t0) cc_final: 0.5839 (m-40) REVERT: C 631 ASP cc_start: 0.6933 (t0) cc_final: 0.6610 (t0) REVERT: C 637 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8581 (m) REVERT: C 790 GLU cc_start: 0.8388 (tt0) cc_final: 0.8025 (tt0) REVERT: C 799 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8438 (mm) REVERT: C 812 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7532 (mmtp) REVERT: C 816 ASP cc_start: 0.7424 (m-30) cc_final: 0.7165 (m-30) REVERT: C 839 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7972 (tp40) REVERT: C 890 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8122 (tt) REVERT: C 1032 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7936 (mttp) REVERT: C 1057 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8696 (m) REVERT: C 1058 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8732 (t) REVERT: C 1061 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7335 (mt-10) REVERT: C 1065 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7133 (t0) REVERT: B 56 ASP cc_start: 0.7786 (t70) cc_final: 0.7501 (t0) REVERT: B 78 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: B 187 ILE cc_start: 0.8264 (tt) cc_final: 0.7971 (tp) REVERT: B 296 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: B 390 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6503 (tt0) REVERT: B 460 MET cc_start: 0.8073 (mtp) cc_final: 0.7392 (mtp) REVERT: B 557 TYR cc_start: 0.8415 (t80) cc_final: 0.8163 (t80) REVERT: B 567 MET cc_start: 0.8374 (mtp) cc_final: 0.8151 (mtp) REVERT: B 586 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.6005 (mp10) REVERT: B 637 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8561 (m) REVERT: B 659 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8258 (t) REVERT: B 790 GLU cc_start: 0.8435 (tt0) cc_final: 0.8014 (tt0) REVERT: B 890 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8134 (tt) REVERT: B 911 GLN cc_start: 0.6426 (OUTLIER) cc_final: 0.6153 (mm-40) REVERT: B 930 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8251 (tptm) REVERT: B 1006 GLN cc_start: 0.7136 (pt0) cc_final: 0.6824 (pp30) REVERT: B 1032 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7937 (mttt) REVERT: B 1057 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8617 (m) REVERT: B 1058 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8782 (t) REVERT: B 1059 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6803 (mm-30) REVERT: B 1061 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7152 (mt-10) REVERT: B 1081 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.7061 (mm-40) outliers start: 267 outliers final: 73 residues processed: 544 average time/residue: 0.6022 time to fit residues: 390.7957 Evaluate side-chains 354 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 244 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 586 GLN Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1059 GLU Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 296 GLN Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 586 GLN Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 812 LYS Chi-restraints excluded: chain C residue 839 GLN Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 1057 THR Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1173 GLN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 296 GLN Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 911 GLN Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 1057 THR Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1059 GLU Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1081 GLN Chi-restraints excluded: chain B residue 1171 LEU Chi-restraints excluded: chain B residue 1173 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 HIS A 285 ASN A 416 ASN A 679 HIS A 686 GLN A 809 ASN A 823 GLN A 904 GLN C 91 GLN C 158 HIS C 285 ASN C 327 HIS C 416 ASN C 686 GLN C 809 ASN C 823 GLN C 904 GLN B 91 GLN B 158 HIS B 285 ASN B 416 ASN B 566 GLN B 679 HIS B 686 GLN B 823 GLN B 904 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.137342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097033 restraints weight = 36041.979| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.59 r_work: 0.2990 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29646 Z= 0.148 Angle : 0.696 14.806 40542 Z= 0.358 Chirality : 0.046 0.478 4773 Planarity : 0.005 0.060 5091 Dihedral : 11.111 87.135 5928 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 5.81 % Allowed : 13.37 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -2.80 (0.12), residues: 3540 helix: -2.43 (0.16), residues: 765 sheet: -0.79 (0.16), residues: 882 loop : -2.16 (0.12), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1091 TYR 0.013 0.001 TYR A 559 PHE 0.016 0.001 PHE C 119 TRP 0.009 0.001 TRP B 215 HIS 0.004 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00336 (29508) covalent geometry : angle 0.64349 (40179) SS BOND : bond 0.00730 ( 51) SS BOND : angle 1.41221 ( 102) hydrogen bonds : bond 0.05453 ( 893) hydrogen bonds : angle 5.65961 ( 2580) link_BETA1-4 : bond 0.00441 ( 30) link_BETA1-4 : angle 1.51536 ( 90) link_NAG-ASN : bond 0.00851 ( 57) link_NAG-ASN : angle 3.91099 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 277 time to evaluate : 1.337 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: A 283 ARG cc_start: 0.6464 (mmm-85) cc_final: 0.5730 (mmm-85) REVERT: A 364 VAL cc_start: 0.7790 (OUTLIER) cc_final: 0.7437 (t) REVERT: A 381 GLU cc_start: 0.8719 (tp30) cc_final: 0.8446 (tp30) REVERT: A 517 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.5172 (p90) REVERT: A 586 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.6568 (mp10) REVERT: A 603 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: A 643 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7352 (p0) REVERT: A 690 MET cc_start: 0.8751 (tpt) cc_final: 0.8374 (mmp) REVERT: A 813 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8012 (tmtm) REVERT: A 819 LYS cc_start: 0.8852 (mttt) cc_final: 0.8603 (mttm) REVERT: A 839 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: A 845 ASN cc_start: 0.8646 (t0) cc_final: 0.8443 (t160) REVERT: A 1006 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7441 (pp30) REVERT: A 1061 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8364 (mt-10) REVERT: C 56 ASP cc_start: 0.8424 (t70) cc_final: 0.8161 (t0) REVERT: C 363 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7531 (pp20) REVERT: C 460 MET cc_start: 0.8981 (mtp) cc_final: 0.8747 (mtp) REVERT: C 517 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5150 (p90) REVERT: C 585 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7633 (mmm) REVERT: C 790 GLU cc_start: 0.8945 (tt0) cc_final: 0.8709 (tm-30) REVERT: C 812 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8427 (mmtm) REVERT: C 813 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8390 (tmtm) REVERT: C 890 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8605 (tt) REVERT: B 187 ILE cc_start: 0.8502 (tt) cc_final: 0.8260 (tp) REVERT: B 210 LYS cc_start: 0.6464 (OUTLIER) cc_final: 0.6058 (tppt) REVERT: B 390 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: B 586 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6873 (mp10) REVERT: B 603 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: B 631 ASP cc_start: 0.7714 (t0) cc_final: 0.7443 (t0) REVERT: B 643 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.6810 (p0) REVERT: B 698 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7287 (mtt90) REVERT: B 911 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6771 (mm110) REVERT: B 940 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8226 (tpt) outliers start: 178 outliers final: 81 residues processed: 417 average time/residue: 0.6240 time to fit residues: 309.4091 Evaluate side-chains 331 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 229 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 586 GLN Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 812 LYS Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1173 GLN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 896 THR Chi-restraints excluded: chain B residue 911 GLN Chi-restraints excluded: chain B residue 940 MET Chi-restraints excluded: chain B residue 1173 GLN Chi-restraints excluded: chain B residue 1196 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 171 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 272 optimal weight: 0.6980 chunk 236 optimal weight: 30.0000 chunk 2 optimal weight: 0.0270 chunk 3 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 279 optimal weight: 4.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 635 ASN A 911 GLN C 115 GLN C 635 ASN C 679 HIS C 809 ASN C 839 GLN C 911 GLN B 809 ASN B 839 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099418 restraints weight = 38128.831| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.75 r_work: 0.3034 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29646 Z= 0.148 Angle : 0.682 17.046 40542 Z= 0.348 Chirality : 0.047 0.525 4773 Planarity : 0.005 0.056 5091 Dihedral : 9.699 86.477 5835 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 5.12 % Allowed : 14.68 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.29 (0.13), residues: 3540 helix: -1.47 (0.18), residues: 747 sheet: -0.55 (0.17), residues: 846 loop : -2.02 (0.12), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 168 TYR 0.011 0.001 TYR A 559 PHE 0.017 0.001 PHE C 119 TRP 0.006 0.001 TRP A 957 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00347 (29508) covalent geometry : angle 0.62995 (40179) SS BOND : bond 0.00506 ( 51) SS BOND : angle 1.44831 ( 102) hydrogen bonds : bond 0.05025 ( 893) hydrogen bonds : angle 5.39993 ( 2580) link_BETA1-4 : bond 0.00398 ( 30) link_BETA1-4 : angle 1.55008 ( 90) link_NAG-ASN : bond 0.00780 ( 57) link_NAG-ASN : angle 3.82343 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 249 time to evaluate : 1.085 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: A 283 ARG cc_start: 0.6484 (mmm-85) cc_final: 0.5895 (mmm-85) REVERT: A 381 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8403 (tp30) REVERT: A 389 GLN cc_start: 0.7846 (mm110) cc_final: 0.7482 (mt0) REVERT: A 517 TYR cc_start: 0.6168 (OUTLIER) cc_final: 0.5185 (p90) REVERT: A 586 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.6710 (mp10) REVERT: A 643 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7298 (p0) REVERT: A 690 MET cc_start: 0.8812 (tpt) cc_final: 0.8478 (mmp) REVERT: A 813 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8907 (tttp) REVERT: A 819 LYS cc_start: 0.8804 (mttt) cc_final: 0.8602 (mttm) REVERT: A 1006 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7441 (pp30) REVERT: C 363 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7581 (pp20) REVERT: C 460 MET cc_start: 0.8933 (mtp) cc_final: 0.8701 (mtp) REVERT: C 517 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5102 (p90) REVERT: C 585 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7641 (mmm) REVERT: C 790 GLU cc_start: 0.8855 (tt0) cc_final: 0.8637 (tm-30) REVERT: C 813 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8376 (tmtm) REVERT: C 890 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8643 (tt) REVERT: C 1006 GLN cc_start: 0.7662 (pt0) cc_final: 0.7376 (pt0) REVERT: B 187 ILE cc_start: 0.8562 (tt) cc_final: 0.8338 (tp) REVERT: B 210 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.5866 (tmtt) REVERT: B 389 GLN cc_start: 0.7926 (mm110) cc_final: 0.7686 (tt0) REVERT: B 585 MET cc_start: 0.8449 (mmm) cc_final: 0.7636 (mmm) REVERT: B 586 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.6505 (mp10) REVERT: B 631 ASP cc_start: 0.7885 (t0) cc_final: 0.7638 (t0) REVERT: B 643 ASN cc_start: 0.7189 (OUTLIER) cc_final: 0.6819 (p0) REVERT: B 859 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7765 (mp10) outliers start: 157 outliers final: 93 residues processed: 371 average time/residue: 0.6079 time to fit residues: 267.6912 Evaluate side-chains 333 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 225 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 586 GLN Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 940 MET Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 617 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1173 GLN Chi-restraints excluded: chain C residue 1196 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 841 GLU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 859 GLN Chi-restraints excluded: chain B residue 896 THR Chi-restraints excluded: chain B residue 1173 GLN Chi-restraints excluded: chain B residue 1196 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 277 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 263 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 GLN A 845 ASN C 679 HIS C 845 ASN C 911 GLN C1097 GLN B 839 GLN B 911 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099667 restraints weight = 38153.849| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.48 r_work: 0.3004 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29646 Z= 0.156 Angle : 0.684 13.711 40542 Z= 0.347 Chirality : 0.047 0.564 4773 Planarity : 0.004 0.050 5091 Dihedral : 9.168 86.498 5814 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 5.38 % Allowed : 14.97 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.99 (0.13), residues: 3540 helix: -0.97 (0.19), residues: 747 sheet: -0.42 (0.17), residues: 837 loop : -1.92 (0.12), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 624 TYR 0.010 0.001 TYR A 929 PHE 0.016 0.001 PHE C 119 TRP 0.006 0.001 TRP A 957 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00373 (29508) covalent geometry : angle 0.63334 (40179) SS BOND : bond 0.00526 ( 51) SS BOND : angle 1.63507 ( 102) hydrogen bonds : bond 0.04861 ( 893) hydrogen bonds : angle 5.30948 ( 2580) link_BETA1-4 : bond 0.00392 ( 30) link_BETA1-4 : angle 1.53738 ( 90) link_NAG-ASN : bond 0.00638 ( 57) link_NAG-ASN : angle 3.70538 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 240 time to evaluate : 1.117 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: A 283 ARG cc_start: 0.6585 (mmm-85) cc_final: 0.5968 (mmm-85) REVERT: A 364 VAL cc_start: 0.7787 (OUTLIER) cc_final: 0.7430 (t) REVERT: A 381 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8413 (tp30) REVERT: A 389 GLN cc_start: 0.7838 (mm110) cc_final: 0.7471 (mt0) REVERT: A 517 TYR cc_start: 0.6133 (OUTLIER) cc_final: 0.5220 (p90) REVERT: A 586 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.6749 (mp10) REVERT: A 603 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: A 643 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7377 (p0) REVERT: A 683 MET cc_start: 0.8551 (mtm) cc_final: 0.8304 (ptp) REVERT: A 813 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8897 (tttp) REVERT: A 819 LYS cc_start: 0.8803 (mttt) cc_final: 0.8590 (mttm) REVERT: A 890 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8609 (tt) REVERT: A 1006 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7449 (pp30) REVERT: C 363 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7512 (pp20) REVERT: C 460 MET cc_start: 0.8940 (mtp) cc_final: 0.8654 (mtp) REVERT: C 517 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.5056 (p90) REVERT: C 813 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8400 (tmtm) REVERT: C 890 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8586 (tt) REVERT: C 1006 GLN cc_start: 0.7819 (pt0) cc_final: 0.7449 (pt0) REVERT: B 210 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.5660 (tmtt) REVERT: B 283 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5916 (mmt90) REVERT: B 389 GLN cc_start: 0.7910 (mm110) cc_final: 0.7663 (tt0) REVERT: B 585 MET cc_start: 0.8500 (mmm) cc_final: 0.8057 (tpp) REVERT: B 586 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.6610 (mp10) REVERT: B 603 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: B 643 ASN cc_start: 0.7202 (OUTLIER) cc_final: 0.6804 (p0) REVERT: B 722 ASP cc_start: 0.8180 (m-30) cc_final: 0.7835 (p0) REVERT: B 859 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: B 1098 ASP cc_start: 0.8475 (m-30) cc_final: 0.8252 (m-30) outliers start: 165 outliers final: 100 residues processed: 371 average time/residue: 0.5792 time to fit residues: 256.9362 Evaluate side-chains 343 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 224 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 586 GLN Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 677 CYS Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 940 MET Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1173 GLN Chi-restraints excluded: chain C residue 1196 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 841 GLU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 859 GLN Chi-restraints excluded: chain B residue 896 THR Chi-restraints excluded: chain B residue 1173 GLN Chi-restraints excluded: chain B residue 1196 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 252 optimal weight: 0.9980 chunk 345 optimal weight: 8.9990 chunk 319 optimal weight: 0.9990 chunk 162 optimal weight: 0.0570 chunk 100 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 911 GLN C 679 HIS B 327 HIS B 635 ASN B 839 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101662 restraints weight = 38164.994| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.47 r_work: 0.3054 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29646 Z= 0.127 Angle : 0.656 13.793 40542 Z= 0.333 Chirality : 0.046 0.516 4773 Planarity : 0.004 0.051 5091 Dihedral : 8.701 85.752 5807 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 5.06 % Allowed : 15.72 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.65 (0.13), residues: 3540 helix: -0.49 (0.19), residues: 747 sheet: -0.33 (0.17), residues: 858 loop : -1.72 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.011 0.001 TYR A 646 PHE 0.018 0.001 PHE C 119 TRP 0.006 0.001 TRP A 957 HIS 0.005 0.001 HIS C 679 Details of bonding type rmsd covalent geometry : bond 0.00296 (29508) covalent geometry : angle 0.60754 (40179) SS BOND : bond 0.00519 ( 51) SS BOND : angle 1.44798 ( 102) hydrogen bonds : bond 0.04398 ( 893) hydrogen bonds : angle 5.18037 ( 2580) link_BETA1-4 : bond 0.00401 ( 30) link_BETA1-4 : angle 1.48537 ( 90) link_NAG-ASN : bond 0.00605 ( 57) link_NAG-ASN : angle 3.59574 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 234 time to evaluate : 1.010 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: A 57 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8485 (m) REVERT: A 283 ARG cc_start: 0.6627 (mmm-85) cc_final: 0.6030 (mmm-85) REVERT: A 364 VAL cc_start: 0.7617 (OUTLIER) cc_final: 0.7232 (t) REVERT: A 381 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8425 (tp30) REVERT: A 389 GLN cc_start: 0.7864 (mm110) cc_final: 0.7548 (mt0) REVERT: A 517 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.5286 (p90) REVERT: A 586 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: A 603 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: A 770 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7082 (pp) REVERT: A 813 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8898 (tttp) REVERT: A 890 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8614 (tt) REVERT: A 1006 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: C 363 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7456 (pp20) REVERT: C 460 MET cc_start: 0.8905 (mtp) cc_final: 0.8605 (mtp) REVERT: C 517 TYR cc_start: 0.6065 (OUTLIER) cc_final: 0.5041 (p90) REVERT: C 585 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7725 (mpp) REVERT: C 813 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8424 (tmtm) REVERT: C 890 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8648 (tt) REVERT: C 1006 GLN cc_start: 0.7623 (pt0) cc_final: 0.7325 (pt0) REVERT: B 168 ARG cc_start: 0.6331 (ptp-170) cc_final: 0.5776 (ptm160) REVERT: B 210 LYS cc_start: 0.6484 (OUTLIER) cc_final: 0.5370 (tmtt) REVERT: B 283 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.5976 (mmt90) REVERT: B 389 GLN cc_start: 0.7887 (mm110) cc_final: 0.7659 (tt0) REVERT: B 585 MET cc_start: 0.8447 (mmm) cc_final: 0.7812 (mmm) REVERT: B 586 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.6506 (mp10) REVERT: B 603 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: B 623 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6258 (pt) REVERT: B 643 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6740 (p0) REVERT: B 722 ASP cc_start: 0.8164 (m-30) cc_final: 0.7843 (p0) REVERT: B 859 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: B 1098 ASP cc_start: 0.8447 (m-30) cc_final: 0.8222 (m-30) outliers start: 155 outliers final: 84 residues processed: 358 average time/residue: 0.6006 time to fit residues: 255.3906 Evaluate side-chains 323 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 217 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 586 GLN Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 677 CYS Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1173 GLN Chi-restraints excluded: chain C residue 1196 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 841 GLU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 859 GLN Chi-restraints excluded: chain B residue 896 THR Chi-restraints excluded: chain B residue 1173 GLN Chi-restraints excluded: chain B residue 1196 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 176 optimal weight: 0.8980 chunk 346 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 238 optimal weight: 0.5980 chunk 286 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 342 optimal weight: 0.0050 chunk 218 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 ASN A 679 HIS C 258 ASN C 434 HIS C 679 HIS B 158 HIS B 839 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100972 restraints weight = 38035.425| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.88 r_work: 0.3039 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 29646 Z= 0.107 Angle : 0.628 13.015 40542 Z= 0.318 Chirality : 0.045 0.406 4773 Planarity : 0.004 0.049 5091 Dihedral : 8.152 84.919 5793 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 4.53 % Allowed : 16.11 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.37 (0.13), residues: 3540 helix: -0.06 (0.20), residues: 744 sheet: -0.27 (0.17), residues: 858 loop : -1.58 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 624 TYR 0.012 0.001 TYR B 647 PHE 0.018 0.001 PHE B 119 TRP 0.007 0.001 TRP B 215 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00241 (29508) covalent geometry : angle 0.57927 (40179) SS BOND : bond 0.00469 ( 51) SS BOND : angle 1.41880 ( 102) hydrogen bonds : bond 0.03919 ( 893) hydrogen bonds : angle 5.04973 ( 2580) link_BETA1-4 : bond 0.00385 ( 30) link_BETA1-4 : angle 1.42368 ( 90) link_NAG-ASN : bond 0.00594 ( 57) link_NAG-ASN : angle 3.50439 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 243 time to evaluate : 1.155 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 57 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8540 (m) REVERT: A 168 ARG cc_start: 0.6401 (ptp-170) cc_final: 0.6151 (ptp-170) REVERT: A 283 ARG cc_start: 0.6494 (mmm-85) cc_final: 0.5879 (mmm-85) REVERT: A 363 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7434 (pp20) REVERT: A 364 VAL cc_start: 0.7617 (OUTLIER) cc_final: 0.7260 (t) REVERT: A 381 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8461 (tp30) REVERT: A 389 GLN cc_start: 0.7824 (mm110) cc_final: 0.7429 (mt0) REVERT: A 517 TYR cc_start: 0.6248 (OUTLIER) cc_final: 0.5379 (p90) REVERT: A 586 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: A 603 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: A 690 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8520 (mmp) REVERT: A 770 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7027 (pp) REVERT: A 809 ASN cc_start: 0.8986 (t0) cc_final: 0.8685 (t0) REVERT: A 897 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8834 (mt) REVERT: A 1006 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7481 (pt0) REVERT: C 187 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8027 (tt) REVERT: C 283 ARG cc_start: 0.7645 (mpt-90) cc_final: 0.6420 (mmm-85) REVERT: C 363 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7408 (pp20) REVERT: C 517 TYR cc_start: 0.6064 (OUTLIER) cc_final: 0.5089 (p90) REVERT: C 585 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7753 (mpp) REVERT: C 603 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: C 813 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8329 (tmtm) REVERT: C 890 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8643 (tt) REVERT: C 1006 GLN cc_start: 0.7565 (pt0) cc_final: 0.7265 (pt0) REVERT: C 1166 ASP cc_start: 0.7679 (t70) cc_final: 0.7304 (t70) REVERT: B 210 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.5809 (tmtt) REVERT: B 283 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.5917 (mmt90) REVERT: B 389 GLN cc_start: 0.7850 (mm110) cc_final: 0.7504 (tt0) REVERT: B 586 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7774 (mm110) REVERT: B 603 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: B 623 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6253 (pt) REVERT: B 631 ASP cc_start: 0.7780 (t0) cc_final: 0.7479 (t0) REVERT: B 809 ASN cc_start: 0.9012 (t0) cc_final: 0.8717 (t0) REVERT: B 859 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7698 (mt0) REVERT: B 897 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8751 (mt) REVERT: B 1098 ASP cc_start: 0.8431 (m-30) cc_final: 0.8183 (m-30) REVERT: B 1173 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6659 (pm20) outliers start: 139 outliers final: 71 residues processed: 352 average time/residue: 0.6194 time to fit residues: 258.1608 Evaluate side-chains 322 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 225 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 586 GLN Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 677 CYS Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 617 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1173 GLN Chi-restraints excluded: chain C residue 1196 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 859 GLN Chi-restraints excluded: chain B residue 896 THR Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1173 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 98 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 117 optimal weight: 0.0010 chunk 131 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 158 HIS A 679 HIS C 158 HIS C 258 ASN C 284 ASN C 679 HIS B 645 ASN B 679 HIS B 839 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100924 restraints weight = 38074.088| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.75 r_work: 0.3047 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29646 Z= 0.135 Angle : 0.646 12.666 40542 Z= 0.327 Chirality : 0.046 0.408 4773 Planarity : 0.004 0.048 5091 Dihedral : 8.028 85.321 5784 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 4.47 % Allowed : 16.44 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.30 (0.13), residues: 3540 helix: -0.03 (0.19), residues: 759 sheet: -0.23 (0.17), residues: 858 loop : -1.53 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.010 0.001 TYR A 929 PHE 0.016 0.001 PHE B 119 TRP 0.013 0.001 TRP B 215 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00322 (29508) covalent geometry : angle 0.59839 (40179) SS BOND : bond 0.00602 ( 51) SS BOND : angle 1.58316 ( 102) hydrogen bonds : bond 0.04282 ( 893) hydrogen bonds : angle 5.02922 ( 2580) link_BETA1-4 : bond 0.00396 ( 30) link_BETA1-4 : angle 1.48760 ( 90) link_NAG-ASN : bond 0.00601 ( 57) link_NAG-ASN : angle 3.49703 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 233 time to evaluate : 1.048 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: A 57 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8512 (m) REVERT: A 168 ARG cc_start: 0.6449 (ptp-170) cc_final: 0.6203 (ptp-170) REVERT: A 283 ARG cc_start: 0.6486 (mmm-85) cc_final: 0.5934 (mmm-85) REVERT: A 363 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7496 (pp20) REVERT: A 364 VAL cc_start: 0.7581 (OUTLIER) cc_final: 0.7214 (t) REVERT: A 381 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8464 (tp30) REVERT: A 389 GLN cc_start: 0.7844 (mm110) cc_final: 0.7494 (mt0) REVERT: A 517 TYR cc_start: 0.6378 (OUTLIER) cc_final: 0.5570 (p90) REVERT: A 586 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6946 (mp10) REVERT: A 603 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: A 770 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.7010 (pp) REVERT: A 809 ASN cc_start: 0.8894 (t0) cc_final: 0.8629 (t0) REVERT: A 816 ASP cc_start: 0.8299 (m-30) cc_final: 0.8060 (m-30) REVERT: A 1006 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: C 155 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8558 (mp) REVERT: C 283 ARG cc_start: 0.7640 (mpt-90) cc_final: 0.6427 (mmm-85) REVERT: C 363 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7503 (pp20) REVERT: C 517 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5308 (p90) REVERT: C 585 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7606 (mmm) REVERT: C 603 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: C 813 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8407 (tmtm) REVERT: C 890 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8687 (tt) REVERT: C 1006 GLN cc_start: 0.7427 (pt0) cc_final: 0.7178 (pt0) REVERT: C 1166 ASP cc_start: 0.7692 (t70) cc_final: 0.7316 (t70) REVERT: B 210 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.5865 (tmtt) REVERT: B 283 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5976 (mmt90) REVERT: B 389 GLN cc_start: 0.7899 (mm110) cc_final: 0.7643 (tt0) REVERT: B 586 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.6712 (mp10) REVERT: B 603 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: B 623 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6207 (pt) REVERT: B 631 ASP cc_start: 0.7814 (t0) cc_final: 0.7523 (t0) REVERT: B 809 ASN cc_start: 0.8952 (t0) cc_final: 0.8659 (t0) REVERT: B 897 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8732 (mt) REVERT: B 1098 ASP cc_start: 0.8420 (m-30) cc_final: 0.8184 (m-30) outliers start: 137 outliers final: 83 residues processed: 340 average time/residue: 0.6036 time to fit residues: 243.0974 Evaluate side-chains 334 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 229 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 586 GLN Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 677 CYS Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 940 MET Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 617 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1173 GLN Chi-restraints excluded: chain C residue 1196 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 841 GLU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 896 THR Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1173 GLN Chi-restraints excluded: chain B residue 1196 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 161 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 206 optimal weight: 0.0000 chunk 350 optimal weight: 6.9990 chunk 333 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 679 HIS C 679 HIS B 679 HIS B 839 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100653 restraints weight = 38039.502| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.78 r_work: 0.3055 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29646 Z= 0.132 Angle : 0.651 13.001 40542 Z= 0.327 Chirality : 0.046 0.379 4773 Planarity : 0.004 0.054 5091 Dihedral : 7.971 85.734 5784 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 4.37 % Allowed : 16.54 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.23 (0.13), residues: 3540 helix: 0.11 (0.20), residues: 759 sheet: -0.22 (0.17), residues: 858 loop : -1.50 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 283 TYR 0.010 0.001 TYR B 647 PHE 0.016 0.001 PHE B 119 TRP 0.005 0.001 TRP A 957 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00314 (29508) covalent geometry : angle 0.59813 (40179) SS BOND : bond 0.00569 ( 51) SS BOND : angle 1.54826 ( 102) hydrogen bonds : bond 0.04293 ( 893) hydrogen bonds : angle 5.02384 ( 2580) link_BETA1-4 : bond 0.00405 ( 30) link_BETA1-4 : angle 1.49491 ( 90) link_NAG-ASN : bond 0.00549 ( 57) link_NAG-ASN : angle 3.70009 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 236 time to evaluate : 1.133 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 57 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8509 (m) REVERT: A 283 ARG cc_start: 0.6467 (mmm-85) cc_final: 0.5839 (mmm-85) REVERT: A 363 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7458 (pp20) REVERT: A 364 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7262 (t) REVERT: A 381 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8479 (tp30) REVERT: A 517 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.5496 (p90) REVERT: A 603 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: A 690 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8518 (mmp) REVERT: A 770 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7007 (pp) REVERT: A 809 ASN cc_start: 0.8928 (t0) cc_final: 0.8643 (t0) REVERT: A 816 ASP cc_start: 0.8285 (m-30) cc_final: 0.8041 (m-30) REVERT: A 1006 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: C 155 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8558 (mp) REVERT: C 173 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7581 (pt) REVERT: C 363 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7430 (pp20) REVERT: C 517 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.5335 (p90) REVERT: C 585 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7798 (mpp) REVERT: C 603 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: C 813 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8425 (tmtm) REVERT: C 890 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8648 (tt) REVERT: C 1006 GLN cc_start: 0.7420 (pt0) cc_final: 0.7158 (pt0) REVERT: C 1166 ASP cc_start: 0.7822 (t70) cc_final: 0.7457 (t70) REVERT: B 210 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.5836 (tmtt) REVERT: B 283 ARG cc_start: 0.6351 (OUTLIER) cc_final: 0.5957 (mmt90) REVERT: B 389 GLN cc_start: 0.7912 (mm110) cc_final: 0.7634 (tt0) REVERT: B 586 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.6960 (mp10) REVERT: B 603 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: B 623 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6416 (pt) REVERT: B 809 ASN cc_start: 0.8977 (t0) cc_final: 0.8772 (t0) REVERT: B 897 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8734 (mt) REVERT: B 1098 ASP cc_start: 0.8411 (m-30) cc_final: 0.8166 (m-30) outliers start: 134 outliers final: 84 residues processed: 344 average time/residue: 0.5866 time to fit residues: 239.5589 Evaluate side-chains 330 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 223 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 940 MET Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 617 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1173 GLN Chi-restraints excluded: chain C residue 1196 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 841 GLU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 896 THR Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1173 GLN Chi-restraints excluded: chain B residue 1196 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 271 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 246 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 203 optimal weight: 0.0170 chunk 94 optimal weight: 4.9990 overall best weight: 1.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 679 HIS A 911 GLN C 679 HIS B 679 HIS B 809 ASN B 911 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.100078 restraints weight = 38058.763| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.74 r_work: 0.3034 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29646 Z= 0.156 Angle : 0.673 13.152 40542 Z= 0.338 Chirality : 0.046 0.377 4773 Planarity : 0.004 0.055 5091 Dihedral : 7.872 86.823 5780 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.35 % Rotamer: Outliers : 4.31 % Allowed : 16.47 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.23 (0.13), residues: 3540 helix: 0.08 (0.19), residues: 762 sheet: -0.24 (0.17), residues: 867 loop : -1.48 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 283 TYR 0.010 0.001 TYR A 929 PHE 0.015 0.001 PHE B 119 TRP 0.006 0.001 TRP B 215 HIS 0.005 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00376 (29508) covalent geometry : angle 0.62081 (40179) SS BOND : bond 0.00576 ( 51) SS BOND : angle 1.62636 ( 102) hydrogen bonds : bond 0.04564 ( 893) hydrogen bonds : angle 5.05606 ( 2580) link_BETA1-4 : bond 0.00411 ( 30) link_BETA1-4 : angle 1.54337 ( 90) link_NAG-ASN : bond 0.00575 ( 57) link_NAG-ASN : angle 3.73586 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 228 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8485 (m) REVERT: A 283 ARG cc_start: 0.6511 (mmm-85) cc_final: 0.5918 (mmm-85) REVERT: A 363 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7509 (pp20) REVERT: A 364 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7239 (t) REVERT: A 381 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8443 (tp30) REVERT: A 517 TYR cc_start: 0.6346 (OUTLIER) cc_final: 0.5557 (p90) REVERT: A 603 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: A 770 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7088 (pp) REVERT: A 809 ASN cc_start: 0.8912 (t0) cc_final: 0.8631 (t0) REVERT: A 816 ASP cc_start: 0.8284 (m-30) cc_final: 0.8047 (m-30) REVERT: A 1006 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7528 (pt0) REVERT: A 1166 ASP cc_start: 0.8014 (t70) cc_final: 0.7656 (t70) REVERT: C 155 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8595 (mp) REVERT: C 363 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7489 (pp20) REVERT: C 517 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.5371 (p90) REVERT: C 585 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7571 (mmm) REVERT: C 603 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: C 813 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8423 (tmtm) REVERT: C 841 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: C 890 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8723 (tt) REVERT: C 1006 GLN cc_start: 0.7439 (pt0) cc_final: 0.7176 (pt0) REVERT: C 1166 ASP cc_start: 0.7863 (t70) cc_final: 0.7495 (t70) REVERT: B 210 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.5852 (tmtt) REVERT: B 283 ARG cc_start: 0.6378 (OUTLIER) cc_final: 0.5973 (mmt90) REVERT: B 389 GLN cc_start: 0.7940 (mm110) cc_final: 0.7623 (tt0) REVERT: B 586 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.6906 (mp10) REVERT: B 603 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: B 897 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8750 (mt) REVERT: B 985 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: B 1098 ASP cc_start: 0.8436 (m-30) cc_final: 0.8194 (m-30) outliers start: 132 outliers final: 86 residues processed: 331 average time/residue: 0.6001 time to fit residues: 234.7266 Evaluate side-chains 329 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 221 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 940 MET Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 841 GLU Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1173 GLN Chi-restraints excluded: chain C residue 1196 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 896 THR Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 985 GLN Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1173 GLN Chi-restraints excluded: chain B residue 1196 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 188 optimal weight: 0.3980 chunk 277 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 336 optimal weight: 3.9990 chunk 309 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 259 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 679 HIS C 679 HIS B 679 HIS B 911 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100984 restraints weight = 37954.910| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.68 r_work: 0.3046 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29646 Z= 0.111 Angle : 0.632 12.714 40542 Z= 0.318 Chirality : 0.045 0.351 4773 Planarity : 0.004 0.056 5091 Dihedral : 7.592 86.181 5779 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.92 % Rotamer: Outliers : 3.42 % Allowed : 17.58 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.07 (0.14), residues: 3540 helix: 0.35 (0.20), residues: 759 sheet: -0.25 (0.17), residues: 870 loop : -1.39 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 283 TYR 0.011 0.001 TYR A 646 PHE 0.019 0.001 PHE B 119 TRP 0.008 0.001 TRP B 261 HIS 0.004 0.001 HIS C 616 Details of bonding type rmsd covalent geometry : bond 0.00254 (29508) covalent geometry : angle 0.58068 (40179) SS BOND : bond 0.00531 ( 51) SS BOND : angle 1.38906 ( 102) hydrogen bonds : bond 0.03927 ( 893) hydrogen bonds : angle 4.97522 ( 2580) link_BETA1-4 : bond 0.00410 ( 30) link_BETA1-4 : angle 1.43895 ( 90) link_NAG-ASN : bond 0.00605 ( 57) link_NAG-ASN : angle 3.62809 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 233 time to evaluate : 1.075 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: A 57 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8496 (m) REVERT: A 168 ARG cc_start: 0.6437 (ptp-170) cc_final: 0.5870 (ptm160) REVERT: A 283 ARG cc_start: 0.6656 (mmm-85) cc_final: 0.6057 (mmm-85) REVERT: A 363 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7529 (pp20) REVERT: A 364 VAL cc_start: 0.7511 (OUTLIER) cc_final: 0.7122 (t) REVERT: A 381 GLU cc_start: 0.8679 (tp30) cc_final: 0.8476 (tp30) REVERT: A 387 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7861 (t) REVERT: A 389 GLN cc_start: 0.7840 (mm110) cc_final: 0.7618 (tt0) REVERT: A 517 TYR cc_start: 0.6316 (OUTLIER) cc_final: 0.5529 (p90) REVERT: A 603 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: A 690 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8565 (mmp) REVERT: A 770 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7095 (pp) REVERT: A 809 ASN cc_start: 0.8888 (t0) cc_final: 0.8616 (t0) REVERT: A 816 ASP cc_start: 0.8326 (m-30) cc_final: 0.8093 (m-30) REVERT: A 897 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8814 (mt) REVERT: A 1006 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: A 1021 ASP cc_start: 0.8303 (m-30) cc_final: 0.7854 (m-30) REVERT: A 1166 ASP cc_start: 0.7998 (t70) cc_final: 0.7625 (t70) REVERT: C 168 ARG cc_start: 0.6184 (ptp-170) cc_final: 0.5915 (ptp-170) REVERT: C 173 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7494 (pt) REVERT: C 187 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8117 (tt) REVERT: C 363 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7529 (pp20) REVERT: C 517 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.5286 (p90) REVERT: C 585 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7615 (mmm) REVERT: C 603 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: C 813 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8435 (tmtm) REVERT: C 841 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: C 890 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8702 (tt) REVERT: C 1006 GLN cc_start: 0.7379 (pt0) cc_final: 0.7169 (pt0) REVERT: C 1166 ASP cc_start: 0.7844 (t70) cc_final: 0.7505 (t70) REVERT: B 283 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.5982 (mmt90) REVERT: B 389 GLN cc_start: 0.7938 (mm110) cc_final: 0.7697 (tt0) REVERT: B 586 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.6793 (mp10) REVERT: B 603 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8019 (tt0) outliers start: 105 outliers final: 67 residues processed: 317 average time/residue: 0.6059 time to fit residues: 227.2789 Evaluate side-chains 315 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 226 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 940 MET Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 517 TYR Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 617 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 841 GLU Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1173 GLN Chi-restraints excluded: chain C residue 1196 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 517 TYR Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 617 ASN Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 841 GLU Chi-restraints excluded: chain B residue 896 THR Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1173 GLN Chi-restraints excluded: chain B residue 1196 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 91 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 301 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 239 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 288 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN C 679 HIS C 809 ASN B 679 HIS B 911 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.101523 restraints weight = 38156.166| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.74 r_work: 0.3056 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29646 Z= 0.114 Angle : 0.634 12.478 40542 Z= 0.318 Chirality : 0.045 0.356 4773 Planarity : 0.004 0.056 5091 Dihedral : 7.380 86.723 5774 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 3.36 % Allowed : 17.65 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.00 (0.14), residues: 3540 helix: 0.45 (0.20), residues: 759 sheet: -0.23 (0.17), residues: 870 loop : -1.35 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 283 TYR 0.011 0.001 TYR B 647 PHE 0.017 0.001 PHE B 119 TRP 0.014 0.001 TRP B 215 HIS 0.004 0.001 HIS B 547 Details of bonding type rmsd covalent geometry : bond 0.00264 (29508) covalent geometry : angle 0.58422 (40179) SS BOND : bond 0.00500 ( 51) SS BOND : angle 1.43024 ( 102) hydrogen bonds : bond 0.03991 ( 893) hydrogen bonds : angle 4.93496 ( 2580) link_BETA1-4 : bond 0.00411 ( 30) link_BETA1-4 : angle 1.44771 ( 90) link_NAG-ASN : bond 0.00580 ( 57) link_NAG-ASN : angle 3.58188 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10051.01 seconds wall clock time: 171 minutes 51.28 seconds (10311.28 seconds total)