Starting phenix.real_space_refine on Mon Aug 25 07:43:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmp_60253/08_2025/8zmp_60253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmp_60253/08_2025/8zmp_60253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zmp_60253/08_2025/8zmp_60253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmp_60253/08_2025/8zmp_60253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zmp_60253/08_2025/8zmp_60253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmp_60253/08_2025/8zmp_60253.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.087 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 132 5.16 5 C 16635 2.51 5 N 4230 2.21 5 O 5178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26175 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8308 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 3 Chain: "B" Number of atoms: 8308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8308 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 3 Chain: "C" Number of atoms: 8308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8308 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 132 Unusual residues: {'EIC': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 132 Unusual residues: {'EIC': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 132 Unusual residues: {'EIC': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.40, per 1000 atoms: 0.21 Number of scatterers: 26175 At special positions: 0 Unit cell: (137.34, 143.88, 167.86, 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 132 16.00 O 5178 8.00 N 4230 7.00 C 16635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 420 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 512 " distance=2.04 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 834 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 160 " distance=2.04 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 420 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 512 " distance=2.04 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 834 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 160 " distance=2.04 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 420 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 512 " distance=2.04 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 658 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 834 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG 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 N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG 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 A1302 " - " ASN A 145 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 358 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A1081 " " NAG A1307 " - " ASN A1117 " " NAG A1308 " - " ASN A 692 " " NAG A1309 " - " ASN A1057 " " NAG B1302 " - " ASN B 145 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 358 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B1081 " " NAG B1307 " - " ASN B1117 " " NAG B1308 " - " ASN B 692 " " NAG B1309 " - " ASN B1057 " " NAG C1302 " - " ASN C 145 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 358 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C1081 " " NAG C1307 " - " ASN C1117 " " NAG C1308 " - " ASN C 692 " " NAG C1309 " - " ASN C1057 " " NAG D 1 " - " ASN A 784 " " NAG E 1 " - " ASN A 159 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN A 228 " " NAG H 1 " - " ASN A 120 " " NAG I 1 " - " ASN A 319 " " NAG J 1 " - " ASN A 66 " " NAG K 1 " - " ASN A 270 " " NAG L 1 " - " ASN A 700 " " NAG M 1 " - " ASN B 784 " " NAG N 1 " - " ASN B 159 " " NAG O 1 " - " ASN B 110 " " NAG P 1 " - " ASN B 228 " " NAG Q 1 " - " ASN B 120 " " NAG R 1 " - " ASN B 319 " " NAG S 1 " - " ASN B 66 " " NAG T 1 " - " ASN B 270 " " NAG U 1 " - " ASN B 700 " " NAG V 1 " - " ASN C 784 " " NAG W 1 " - " ASN C 159 " " NAG X 1 " - " ASN C 110 " " NAG Y 1 " - " ASN C 228 " " NAG Z 1 " - " ASN C 120 " " NAG a 1 " - " ASN C 319 " " NAG b 1 " - " ASN C 66 " " NAG c 1 " - " ASN C 270 " " NAG d 1 " - " ASN C 700 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 864.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5988 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 54 sheets defined 22.9% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.655A pdb=" N VAL A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 358 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.369A pdb=" N ASN A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 377 " --> pdb=" O LYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 731 through 739 removed outlier: 4.071A pdb=" N LEU A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 738 " --> pdb=" O ASN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 766 removed outlier: 4.318A pdb=" N GLN A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 746 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 761 " --> pdb=" O GLN A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.743A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 825 Processing helix chain 'A' and resid 826 through 830 Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.524A pdb=" N GLY A 872 " --> pdb=" O TRP A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 896 through 924 removed outlier: 3.675A pdb=" N TYR A 900 " --> pdb=" O GLN A 896 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS A 904 " --> pdb=" O TYR A 900 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 948 removed outlier: 3.747A pdb=" N VAL A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 942 " --> pdb=" O ASN A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 967 Processing helix chain 'A' and resid 968 through 1016 removed outlier: 4.293A pdb=" N VAL A 974 " --> pdb=" O VAL A 970 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A1000 " --> pdb=" O ILE A 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 352 through 358 removed outlier: 3.655A pdb=" N VAL B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B 358 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.368A pdb=" N ASN B 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 731 through 739 removed outlier: 4.072A pdb=" N LEU B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 738 " --> pdb=" O ASN B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 766 removed outlier: 4.318A pdb=" N GLN B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 746 " --> pdb=" O PHE B 742 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 761 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 809 removed outlier: 3.743A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 825 Processing helix chain 'B' and resid 826 through 830 Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 849 through 867 Processing helix chain 'B' and resid 869 through 873 removed outlier: 3.524A pdb=" N GLY B 872 " --> pdb=" O TRP B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 896 through 924 removed outlier: 3.675A pdb=" N TYR B 900 " --> pdb=" O GLN B 896 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LYS B 904 " --> pdb=" O TYR B 900 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN B 905 " --> pdb=" O GLU B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 948 removed outlier: 3.747A pdb=" N VAL B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 935 " --> pdb=" O LEU B 931 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 942 " --> pdb=" O ASN B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 967 Processing helix chain 'B' and resid 968 through 1016 removed outlier: 4.293A pdb=" N VAL B 974 " --> pdb=" O VAL B 970 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN B 975 " --> pdb=" O GLU B 971 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B1000 " --> pdb=" O ILE B 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.655A pdb=" N VAL C 355 " --> pdb=" O ASP C 352 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN C 358 " --> pdb=" O VAL C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.369A pdb=" N ASN C 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 377 " --> pdb=" O LYS C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 720 through 725 Processing helix chain 'C' and resid 731 through 739 removed outlier: 4.071A pdb=" N LEU C 735 " --> pdb=" O GLU C 731 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN C 738 " --> pdb=" O ASN C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 766 removed outlier: 4.319A pdb=" N GLN C 745 " --> pdb=" O SER C 741 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 746 " --> pdb=" O PHE C 742 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 761 " --> pdb=" O GLN C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 809 removed outlier: 3.743A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 Processing helix chain 'C' and resid 826 through 830 Processing helix chain 'C' and resid 831 through 838 Processing helix chain 'C' and resid 849 through 867 Processing helix chain 'C' and resid 869 through 873 removed outlier: 3.524A pdb=" N GLY C 872 " --> pdb=" O TRP C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 891 Processing helix chain 'C' and resid 896 through 924 removed outlier: 3.674A pdb=" N TYR C 900 " --> pdb=" O GLN C 896 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS C 904 " --> pdb=" O TYR C 900 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN C 905 " --> pdb=" O GLU C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 948 removed outlier: 3.747A pdb=" N VAL C 934 " --> pdb=" O LYS C 930 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 935 " --> pdb=" O LEU C 931 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 942 " --> pdb=" O ASN C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 967 Processing helix chain 'C' and resid 968 through 1016 removed outlier: 4.293A pdb=" N VAL C 974 " --> pdb=" O VAL C 970 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN C 975 " --> pdb=" O GLU C 971 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C1000 " --> pdb=" O ILE C 996 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.585A pdb=" N THR A 32 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN A 66 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TYR A 257 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 181 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU A 195 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS A 222 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 197 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR A 201 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA A 216 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 41 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 60 removed outlier: 4.344A pdb=" N ASP A 275 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.189A pdb=" N GLY A 101 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 128 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 162 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.613A pdb=" N LEU A 142 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 147 " --> pdb=" O LEU A 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 6.562A pdb=" N LYS A 312 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASN A 529 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 314 " --> pdb=" O ASN A 529 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 535 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 342 through 346 removed outlier: 4.068A pdb=" N GLU A 342 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 387 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 383 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 511 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N CYS A 349 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 342 through 346 removed outlier: 4.068A pdb=" N GLU A 342 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 387 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 383 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 383 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 501 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA A 385 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 499 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER A 387 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 497 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 389 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR A 495 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 440 through 442 Processing sheet with id=AB2, first strand: chain 'A' and resid 552 through 553 removed outlier: 7.139A pdb=" N PHE A 552 " --> pdb=" O PHE B 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 641 through 642 removed outlier: 6.456A pdb=" N GLU A 641 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N THR A 679 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 651 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 684 through 686 removed outlier: 6.629A pdb=" N ALA A 684 " --> pdb=" O MET B 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 696 Processing sheet with id=AB6, first strand: chain 'A' and resid 700 through 711 removed outlier: 6.519A pdb=" N ASN A 700 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.570A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 770 through 772 removed outlier: 3.526A pdb=" N SER C 686 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AC1, first strand: chain 'A' and resid 1064 through 1065 removed outlier: 3.780A pdb=" N ILE A1064 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A1070 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1077 through 1080 Processing sheet with id=AC3, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.585A pdb=" N THR B 32 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN B 66 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TYR B 257 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 181 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU B 195 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS B 222 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 197 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR B 201 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA B 216 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL B 41 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 53 through 60 removed outlier: 4.344A pdb=" N ASP B 275 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.189A pdb=" N GLY B 101 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 128 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE B 162 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.612A pdb=" N LEU B 142 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 147 " --> pdb=" O LEU B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 299 through 302 Processing sheet with id=AC8, first strand: chain 'B' and resid 312 through 316 removed outlier: 6.562A pdb=" N LYS B 312 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASN B 529 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 314 " --> pdb=" O ASN B 529 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 535 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 342 through 346 removed outlier: 4.069A pdb=" N GLU B 342 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 387 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 511 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N CYS B 349 " --> pdb=" O CYS B 512 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 342 through 346 removed outlier: 4.069A pdb=" N GLU B 342 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 387 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL B 383 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER B 501 " --> pdb=" O VAL B 383 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 385 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 499 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B 387 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 497 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 389 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR B 495 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 440 through 442 Processing sheet with id=AD3, first strand: chain 'B' and resid 552 through 553 removed outlier: 7.130A pdb=" N PHE B 552 " --> pdb=" O PHE C 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 641 through 642 removed outlier: 6.457A pdb=" N GLU B 641 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N THR B 679 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 651 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 684 through 686 removed outlier: 6.622A pdb=" N ALA B 684 " --> pdb=" O MET C 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 694 through 696 Processing sheet with id=AD7, first strand: chain 'B' and resid 700 through 711 removed outlier: 6.519A pdb=" N ASN B 700 " --> pdb=" O SER B1053 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.570A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AE1, first strand: chain 'B' and resid 1064 through 1065 removed outlier: 3.779A pdb=" N ILE B1064 " --> pdb=" O TYR B1071 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B1070 " --> pdb=" O SER B1106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1077 through 1080 Processing sheet with id=AE3, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.585A pdb=" N THR C 32 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN C 66 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N TYR C 257 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 181 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU C 195 " --> pdb=" O LYS C 222 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS C 222 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 197 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR C 201 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA C 216 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL C 41 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 53 through 60 removed outlier: 4.344A pdb=" N ASP C 275 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.190A pdb=" N GLY C 101 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 128 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 162 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.613A pdb=" N LEU C 142 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR C 147 " --> pdb=" O LEU C 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 299 through 302 Processing sheet with id=AE8, first strand: chain 'C' and resid 312 through 316 removed outlier: 6.562A pdb=" N LYS C 312 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASN C 529 " --> pdb=" O LYS C 312 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL C 314 " --> pdb=" O ASN C 529 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 535 " --> pdb=" O PHE C 528 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 342 through 346 removed outlier: 4.068A pdb=" N GLU C 342 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER C 387 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 511 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N CYS C 349 " --> pdb=" O CYS C 512 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 342 through 346 removed outlier: 4.068A pdb=" N GLU C 342 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER C 387 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL C 383 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER C 501 " --> pdb=" O VAL C 383 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA C 385 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 499 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER C 387 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C 497 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL C 389 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR C 495 " --> pdb=" O VAL C 389 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 440 through 442 Processing sheet with id=AF3, first strand: chain 'C' and resid 641 through 642 removed outlier: 6.456A pdb=" N GLU C 641 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N THR C 679 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 651 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 694 through 696 Processing sheet with id=AF5, first strand: chain 'C' and resid 700 through 711 removed outlier: 6.518A pdb=" N ASN C 700 " --> pdb=" O SER C1053 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.570A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AF8, first strand: chain 'C' and resid 1064 through 1065 removed outlier: 3.780A pdb=" N ILE C1064 " --> pdb=" O TYR C1071 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA C1070 " --> pdb=" O SER C1106 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1077 through 1080 908 hydrogen bonds defined for protein. 2508 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: 4.52 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4227 1.30 - 1.43: 7583 1.43 - 1.57: 14770 1.57 - 1.70: 0 1.70 - 1.83: 174 Bond restraints: 26754 Sorted by residual: bond pdb=" CA LEU C 210 " pdb=" C LEU C 210 " ideal model delta sigma weight residual 1.522 1.446 0.077 1.08e-02 8.57e+03 5.02e+01 bond pdb=" CA ALA A 128 " pdb=" C ALA A 128 " ideal model delta sigma weight residual 1.520 1.438 0.082 1.16e-02 7.43e+03 5.02e+01 bond pdb=" CA LEU A 210 " pdb=" C LEU A 210 " ideal model delta sigma weight residual 1.522 1.446 0.077 1.08e-02 8.57e+03 5.02e+01 bond pdb=" CA LEU B 210 " pdb=" C LEU B 210 " ideal model delta sigma weight residual 1.522 1.446 0.076 1.08e-02 8.57e+03 5.02e+01 bond pdb=" CA ALA B 128 " pdb=" C ALA B 128 " ideal model delta sigma weight residual 1.520 1.438 0.082 1.16e-02 7.43e+03 5.01e+01 ... (remaining 26749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 35434 1.91 - 3.82: 743 3.82 - 5.73: 132 5.73 - 7.64: 27 7.64 - 9.55: 33 Bond angle restraints: 36369 Sorted by residual: angle pdb=" N ASN A 159 " pdb=" CA ASN A 159 " pdb=" C ASN A 159 " ideal model delta sigma weight residual 109.96 119.21 -9.25 1.50e+00 4.44e-01 3.80e+01 angle pdb=" N ASN C 159 " pdb=" CA ASN C 159 " pdb=" C ASN C 159 " ideal model delta sigma weight residual 109.96 119.19 -9.23 1.50e+00 4.44e-01 3.79e+01 angle pdb=" N ASN B 159 " pdb=" CA ASN B 159 " pdb=" C ASN B 159 " ideal model delta sigma weight residual 109.96 119.17 -9.21 1.50e+00 4.44e-01 3.77e+01 angle pdb=" N ILE B 153 " pdb=" CA ILE B 153 " pdb=" C ILE B 153 " ideal model delta sigma weight residual 112.96 106.92 6.04 1.00e+00 1.00e+00 3.65e+01 angle pdb=" N ILE A 153 " pdb=" CA ILE A 153 " pdb=" C ILE A 153 " ideal model delta sigma weight residual 112.96 106.93 6.03 1.00e+00 1.00e+00 3.63e+01 ... (remaining 36364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.90: 15597 23.90 - 47.80: 1232 47.80 - 71.70: 181 71.70 - 95.60: 18 95.60 - 119.49: 48 Dihedral angle restraints: 17076 sinusoidal: 7776 harmonic: 9300 Sorted by residual: dihedral pdb=" CB CYS A 726 " pdb=" SG CYS A 726 " pdb=" SG CYS A 732 " pdb=" CB CYS A 732 " ideal model delta sinusoidal sigma weight residual -86.00 -148.77 62.77 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS B 726 " pdb=" SG CYS B 726 " pdb=" SG CYS B 732 " pdb=" CB CYS B 732 " ideal model delta sinusoidal sigma weight residual -86.00 -148.74 62.74 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS C 726 " pdb=" SG CYS C 726 " pdb=" SG CYS C 732 " pdb=" CB CYS C 732 " ideal model delta sinusoidal sigma weight residual -86.00 -148.74 62.74 1 1.00e+01 1.00e-02 5.20e+01 ... (remaining 17073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4089 0.098 - 0.197: 240 0.197 - 0.295: 12 0.295 - 0.394: 3 0.394 - 0.492: 3 Chirality restraints: 4347 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN C 159 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 159 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 159 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 4344 not shown) Planarity restraints: 4665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 206 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C ALA B 206 " 0.052 2.00e-02 2.50e+03 pdb=" O ALA B 206 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA B 207 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 206 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C ALA A 206 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA A 206 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 207 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 206 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C ALA C 206 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA C 206 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 207 " -0.017 2.00e-02 2.50e+03 ... (remaining 4662 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4502 2.77 - 3.30: 23517 3.30 - 3.83: 41095 3.83 - 4.37: 47427 4.37 - 4.90: 84970 Nonbonded interactions: 201511 Sorted by model distance: nonbonded pdb=" OH TYR C 42 " pdb=" O HIS C 59 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR B 42 " pdb=" O HIS B 59 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR A 42 " pdb=" O HIS A 59 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 592 " pdb=" OE1 GLU B 594 " model vdw 2.239 3.040 nonbonded pdb=" OG SER A 592 " pdb=" OE1 GLU A 594 " model vdw 2.239 3.040 ... (remaining 201506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'N' selection = chain 'W' } 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.620 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.005 0.083 26883 Z= 0.337 Angle : 0.737 9.552 36714 Z= 0.394 Chirality : 0.049 0.492 4347 Planarity : 0.004 0.040 4614 Dihedral : 16.900 119.495 10962 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.41 % Allowed : 20.24 % Favored : 74.35 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.14), residues: 3174 helix: 0.60 (0.21), residues: 678 sheet: 0.23 (0.20), residues: 642 loop : -1.96 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 127 TYR 0.009 0.001 TYR B1050 PHE 0.010 0.001 PHE C 154 TRP 0.010 0.001 TRP C 246 HIS 0.001 0.000 HIS C1066 Details of bonding type rmsd covalent geometry : bond 0.00485 (26754) covalent geometry : angle 0.69147 (36369) SS BOND : bond 0.00389 ( 42) SS BOND : angle 1.23375 ( 84) hydrogen bonds : bond 0.20692 ( 899) hydrogen bonds : angle 7.21657 ( 2508) link_ALPHA1-3 : bond 0.00115 ( 3) link_ALPHA1-3 : angle 2.06071 ( 9) link_BETA1-4 : bond 0.01114 ( 33) link_BETA1-4 : angle 3.03324 ( 99) link_NAG-ASN : bond 0.00757 ( 51) link_NAG-ASN : angle 3.11064 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 225 time to evaluate : 0.902 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 23 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.5520 (m-10) REVERT: A 25 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.6880 (p0) REVERT: A 94 GLU cc_start: 0.7213 (pt0) cc_final: 0.6796 (pt0) REVERT: A 297 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7371 (p0) REVERT: A 377 ASP cc_start: 0.8442 (m-30) cc_final: 0.8204 (m-30) REVERT: A 413 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8876 (mt) REVERT: A 519 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8003 (t0) REVERT: A 641 GLU cc_start: 0.7826 (mp0) cc_final: 0.7495 (mm-30) REVERT: A 657 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8726 (mm) REVERT: A 731 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7834 (mt-10) REVERT: A 793 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7441 (pp) REVERT: A 975 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.6444 (mm-40) REVERT: B 25 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.6892 (p0) REVERT: B 73 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.6186 (p90) REVERT: B 131 PHE cc_start: 0.8062 (m-10) cc_final: 0.7740 (m-80) REVERT: B 138 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: B 413 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8911 (mt) REVERT: B 519 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8004 (t0) REVERT: B 641 GLU cc_start: 0.8016 (mp0) cc_final: 0.7773 (mm-30) REVERT: B 657 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8560 (mm) REVERT: B 793 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7735 (pp) REVERT: B 975 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.6876 (mm-40) REVERT: B 1012 MET cc_start: 0.8915 (tpp) cc_final: 0.8685 (ttm) REVERT: C 23 PHE cc_start: 0.6293 (OUTLIER) cc_final: 0.5829 (m-10) REVERT: C 25 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6863 (p0) REVERT: C 94 GLU cc_start: 0.7247 (pt0) cc_final: 0.6485 (pt0) REVERT: C 131 PHE cc_start: 0.8196 (m-10) cc_final: 0.7948 (m-10) REVERT: C 138 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: C 232 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8230 (p90) REVERT: C 297 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7721 (p0) REVERT: C 413 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8829 (mt) REVERT: C 519 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8089 (t0) REVERT: C 641 GLU cc_start: 0.7870 (mp0) cc_final: 0.7650 (mm-30) REVERT: C 657 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8539 (mm) REVERT: C 731 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7853 (mt-10) REVERT: C 793 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7537 (pp) REVERT: C 926 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7921 (p) REVERT: C 975 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7745 (mm-40) REVERT: C 1012 MET cc_start: 0.9014 (tpp) cc_final: 0.8710 (ttm) outliers start: 150 outliers final: 106 residues processed: 348 average time/residue: 0.1269 time to fit residues: 74.4898 Evaluate side-chains 332 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 199 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 770 GLN Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 952 ASN Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 975 GLN Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 975 GLN Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1119 THR Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 657 ILE Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 770 GLN Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 550 GLN A 819 GLN ** A 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 819 GLN B 938 ASN C 550 GLN C 819 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101268 restraints weight = 39831.184| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.71 r_work: 0.3046 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26883 Z= 0.124 Angle : 0.657 9.069 36714 Z= 0.304 Chirality : 0.047 0.351 4347 Planarity : 0.004 0.044 4614 Dihedral : 12.367 102.411 5504 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.67 % Allowed : 18.40 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.14), residues: 3174 helix: 0.90 (0.20), residues: 702 sheet: 0.62 (0.20), residues: 648 loop : -1.87 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 39 TYR 0.020 0.001 TYR A1050 PHE 0.017 0.001 PHE B1093 TRP 0.009 0.001 TRP A 424 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00275 (26754) covalent geometry : angle 0.59986 (36369) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.02787 ( 84) hydrogen bonds : bond 0.04197 ( 899) hydrogen bonds : angle 5.31778 ( 2508) link_ALPHA1-3 : bond 0.00559 ( 3) link_ALPHA1-3 : angle 3.85481 ( 9) link_BETA1-4 : bond 0.01049 ( 33) link_BETA1-4 : angle 3.00962 ( 99) link_NAG-ASN : bond 0.00618 ( 51) link_NAG-ASN : angle 3.28963 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 208 time to evaluate : 0.921 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 23 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.5700 (m-10) REVERT: A 25 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6977 (p0) REVERT: A 94 GLU cc_start: 0.7341 (pt0) cc_final: 0.6509 (pt0) REVERT: A 413 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8854 (mt) REVERT: A 519 ASP cc_start: 0.8435 (t0) cc_final: 0.8145 (t0) REVERT: A 641 GLU cc_start: 0.7906 (mp0) cc_final: 0.7581 (mm-30) REVERT: A 793 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7460 (pp) REVERT: A 933 ASP cc_start: 0.8921 (m-30) cc_final: 0.8574 (m-30) REVERT: B 73 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.6158 (p90) REVERT: B 131 PHE cc_start: 0.8149 (m-10) cc_final: 0.7700 (m-80) REVERT: B 138 PHE cc_start: 0.8440 (m-80) cc_final: 0.8126 (m-10) REVERT: B 413 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8884 (mt) REVERT: B 641 GLU cc_start: 0.8077 (mp0) cc_final: 0.7835 (mm-30) REVERT: B 793 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7753 (pp) REVERT: B 827 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7494 (mt) REVERT: B 933 ASP cc_start: 0.8851 (m-30) cc_final: 0.8581 (t0) REVERT: C 23 PHE cc_start: 0.6311 (OUTLIER) cc_final: 0.5763 (m-10) REVERT: C 25 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6888 (p0) REVERT: C 94 GLU cc_start: 0.7090 (pt0) cc_final: 0.6389 (pt0) REVERT: C 232 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8494 (p90) REVERT: C 413 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8845 (mt) REVERT: C 519 ASP cc_start: 0.8578 (t0) cc_final: 0.8257 (t0) REVERT: C 641 GLU cc_start: 0.7999 (mp0) cc_final: 0.7777 (mm-30) REVERT: C 731 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8136 (mt-10) REVERT: C 793 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7449 (pp) outliers start: 185 outliers final: 119 residues processed: 367 average time/residue: 0.1478 time to fit residues: 90.8227 Evaluate side-chains 325 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 193 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 952 ASN Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 827 ILE Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 512 CYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 550 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 146 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN ** A 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN C 480 ASN C 890 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097074 restraints weight = 40433.064| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.93 r_work: 0.2958 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 26883 Z= 0.209 Angle : 0.704 9.866 36714 Z= 0.331 Chirality : 0.048 0.347 4347 Planarity : 0.004 0.037 4614 Dihedral : 10.522 89.773 5437 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 6.31 % Allowed : 18.83 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.14), residues: 3174 helix: 0.89 (0.21), residues: 702 sheet: 0.43 (0.20), residues: 681 loop : -1.80 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 39 TYR 0.021 0.001 TYR C1050 PHE 0.014 0.001 PHE A 910 TRP 0.011 0.001 TRP A 424 HIS 0.006 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00507 (26754) covalent geometry : angle 0.64677 (36369) SS BOND : bond 0.00506 ( 42) SS BOND : angle 1.54686 ( 84) hydrogen bonds : bond 0.04881 ( 899) hydrogen bonds : angle 5.09155 ( 2508) link_ALPHA1-3 : bond 0.00458 ( 3) link_ALPHA1-3 : angle 3.79854 ( 9) link_BETA1-4 : bond 0.01098 ( 33) link_BETA1-4 : angle 3.10562 ( 99) link_NAG-ASN : bond 0.00558 ( 51) link_NAG-ASN : angle 3.31682 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 192 time to evaluate : 1.045 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 25 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6775 (p0) REVERT: A 94 GLU cc_start: 0.7643 (pt0) cc_final: 0.6800 (pt0) REVERT: A 413 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8646 (mp) REVERT: A 432 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9121 (p) REVERT: A 519 ASP cc_start: 0.8523 (t0) cc_final: 0.8169 (t0) REVERT: A 641 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: A 793 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7603 (pp) REVERT: B 73 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.6077 (p90) REVERT: B 138 PHE cc_start: 0.8496 (m-80) cc_final: 0.7981 (m-80) REVERT: B 415 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8601 (t0) REVERT: B 432 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.8999 (p) REVERT: B 641 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: B 793 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7759 (pp) REVERT: B 933 ASP cc_start: 0.8988 (m-30) cc_final: 0.8699 (t0) REVERT: C 23 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.5859 (m-10) REVERT: C 25 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6887 (p0) REVERT: C 94 GLU cc_start: 0.7275 (pt0) cc_final: 0.6597 (pt0) REVERT: C 232 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8568 (p90) REVERT: C 413 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8887 (mt) REVERT: C 432 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.8994 (p) REVERT: C 519 ASP cc_start: 0.8611 (t0) cc_final: 0.8252 (t0) REVERT: C 641 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7813 (mm-30) REVERT: C 793 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7476 (pp) outliers start: 175 outliers final: 121 residues processed: 346 average time/residue: 0.1546 time to fit residues: 90.4346 Evaluate side-chains 313 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 175 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 952 ASN Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 512 CYS Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 276 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 315 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 ASN B 890 ASN ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097752 restraints weight = 40104.089| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.82 r_work: 0.2969 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26883 Z= 0.152 Angle : 0.664 8.951 36714 Z= 0.308 Chirality : 0.047 0.355 4347 Planarity : 0.004 0.037 4614 Dihedral : 9.872 69.178 5417 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 6.13 % Allowed : 19.99 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.15), residues: 3174 helix: 0.86 (0.20), residues: 729 sheet: 0.34 (0.20), residues: 714 loop : -1.83 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 564 TYR 0.019 0.001 TYR A1050 PHE 0.013 0.001 PHE B 630 TRP 0.010 0.001 TRP A 424 HIS 0.003 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00360 (26754) covalent geometry : angle 0.60419 (36369) SS BOND : bond 0.00464 ( 42) SS BOND : angle 1.26301 ( 84) hydrogen bonds : bond 0.04321 ( 899) hydrogen bonds : angle 4.87990 ( 2508) link_ALPHA1-3 : bond 0.01065 ( 3) link_ALPHA1-3 : angle 3.05090 ( 9) link_BETA1-4 : bond 0.01137 ( 33) link_BETA1-4 : angle 3.13642 ( 99) link_NAG-ASN : bond 0.00596 ( 51) link_NAG-ASN : angle 3.33118 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 177 time to evaluate : 1.039 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 25 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6831 (p0) REVERT: A 94 GLU cc_start: 0.7662 (pt0) cc_final: 0.6836 (pt0) REVERT: A 136 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8364 (t0) REVERT: A 413 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8750 (mt) REVERT: A 519 ASP cc_start: 0.8514 (t0) cc_final: 0.8163 (t0) REVERT: A 641 GLU cc_start: 0.8020 (mp0) cc_final: 0.7692 (mm-30) REVERT: A 793 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7587 (pp) REVERT: B 73 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.6035 (p90) REVERT: B 138 PHE cc_start: 0.8481 (m-80) cc_final: 0.7974 (m-80) REVERT: B 432 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9009 (p) REVERT: B 793 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7748 (pp) REVERT: B 933 ASP cc_start: 0.8960 (m-30) cc_final: 0.8703 (t0) REVERT: C 25 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.6852 (p0) REVERT: C 94 GLU cc_start: 0.7233 (pt0) cc_final: 0.6522 (pt0) REVERT: C 138 PHE cc_start: 0.8514 (m-80) cc_final: 0.7401 (m-10) REVERT: C 232 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8564 (p90) REVERT: C 413 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8813 (mt) REVERT: C 432 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9016 (p) REVERT: C 519 ASP cc_start: 0.8628 (t0) cc_final: 0.8271 (t0) REVERT: C 793 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7466 (pp) outliers start: 170 outliers final: 124 residues processed: 331 average time/residue: 0.1536 time to fit residues: 85.7788 Evaluate side-chains 305 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 169 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 14 optimal weight: 5.9990 chunk 286 optimal weight: 0.0980 chunk 179 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 160 optimal weight: 0.2980 chunk 74 optimal weight: 0.0770 chunk 240 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.130803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098211 restraints weight = 39930.817| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.80 r_work: 0.2973 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26883 Z= 0.141 Angle : 0.648 8.861 36714 Z= 0.301 Chirality : 0.047 0.358 4347 Planarity : 0.004 0.036 4614 Dihedral : 9.319 55.163 5407 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.24 % Allowed : 20.20 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.15), residues: 3174 helix: 0.96 (0.20), residues: 729 sheet: 0.37 (0.20), residues: 714 loop : -1.76 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 454 TYR 0.019 0.001 TYR A1050 PHE 0.021 0.001 PHE A 630 TRP 0.009 0.001 TRP A 424 HIS 0.003 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00334 (26754) covalent geometry : angle 0.58782 (36369) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.20764 ( 84) hydrogen bonds : bond 0.04121 ( 899) hydrogen bonds : angle 4.73891 ( 2508) link_ALPHA1-3 : bond 0.01310 ( 3) link_ALPHA1-3 : angle 2.38085 ( 9) link_BETA1-4 : bond 0.01148 ( 33) link_BETA1-4 : angle 3.12989 ( 99) link_NAG-ASN : bond 0.00594 ( 51) link_NAG-ASN : angle 3.32111 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 175 time to evaluate : 0.969 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 25 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6872 (p0) REVERT: A 94 GLU cc_start: 0.7604 (pt0) cc_final: 0.6750 (pt0) REVERT: A 136 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8332 (t0) REVERT: A 413 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8759 (mt) REVERT: A 415 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8698 (t0) REVERT: A 519 ASP cc_start: 0.8505 (t0) cc_final: 0.8145 (t0) REVERT: A 641 GLU cc_start: 0.7972 (mp0) cc_final: 0.7605 (mm-30) REVERT: A 793 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7676 (pp) REVERT: B 73 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5975 (p90) REVERT: B 94 GLU cc_start: 0.7268 (pt0) cc_final: 0.7042 (pt0) REVERT: B 138 PHE cc_start: 0.8480 (m-80) cc_final: 0.8021 (m-80) REVERT: B 152 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7483 (m-10) REVERT: B 415 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8659 (t0) REVERT: B 432 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8979 (p) REVERT: B 464 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8447 (p0) REVERT: B 519 ASP cc_start: 0.8536 (t0) cc_final: 0.8191 (t0) REVERT: B 793 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7762 (pp) REVERT: B 933 ASP cc_start: 0.8948 (m-30) cc_final: 0.8698 (t0) REVERT: C 23 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.5820 (m-10) REVERT: C 25 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6904 (p0) REVERT: C 232 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8542 (p90) REVERT: C 413 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8882 (mt) REVERT: C 432 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9020 (p) REVERT: C 519 ASP cc_start: 0.8610 (t0) cc_final: 0.8243 (t0) REVERT: C 770 GLN cc_start: 0.8413 (mp10) cc_final: 0.8207 (mp10) REVERT: C 793 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7397 (pp) outliers start: 173 outliers final: 128 residues processed: 331 average time/residue: 0.1462 time to fit residues: 82.1029 Evaluate side-chains 316 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 171 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 298 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.091211 restraints weight = 40866.540| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.97 r_work: 0.2857 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 26883 Z= 0.302 Angle : 0.773 13.424 36714 Z= 0.371 Chirality : 0.051 0.359 4347 Planarity : 0.004 0.042 4614 Dihedral : 9.510 52.576 5402 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.82 % Allowed : 20.20 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.14), residues: 3174 helix: 0.62 (0.20), residues: 726 sheet: 0.29 (0.20), residues: 720 loop : -1.90 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 396 TYR 0.022 0.002 TYR C1050 PHE 0.020 0.002 PHE A 910 TRP 0.014 0.002 TRP A 424 HIS 0.008 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00745 (26754) covalent geometry : angle 0.71656 (36369) SS BOND : bond 0.00565 ( 42) SS BOND : angle 2.05187 ( 84) hydrogen bonds : bond 0.05568 ( 899) hydrogen bonds : angle 5.07056 ( 2508) link_ALPHA1-3 : bond 0.00593 ( 3) link_ALPHA1-3 : angle 1.98237 ( 9) link_BETA1-4 : bond 0.01132 ( 33) link_BETA1-4 : angle 3.32052 ( 99) link_NAG-ASN : bond 0.00519 ( 51) link_NAG-ASN : angle 3.43003 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 174 time to evaluate : 1.163 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 25 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6821 (p0) REVERT: A 94 GLU cc_start: 0.7729 (pt0) cc_final: 0.7022 (pt0) REVERT: A 136 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8365 (t0) REVERT: A 415 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8753 (t0) REVERT: A 519 ASP cc_start: 0.8568 (t0) cc_final: 0.8200 (t0) REVERT: A 641 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: A 793 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7832 (pp) REVERT: B 138 PHE cc_start: 0.8570 (m-80) cc_final: 0.7972 (m-80) REVERT: B 152 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: B 265 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9176 (mt) REVERT: B 415 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8680 (t0) REVERT: B 432 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9036 (p) REVERT: B 464 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8485 (p0) REVERT: B 600 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7367 (mp10) REVERT: B 641 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7922 (mm-30) REVERT: B 731 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8298 (tp30) REVERT: C 23 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.5920 (m-10) REVERT: C 25 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6892 (p0) REVERT: C 232 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8572 (p90) REVERT: C 413 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8927 (mt) REVERT: C 600 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: C 641 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7976 (mm-30) REVERT: C 710 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8757 (mtp) REVERT: C 793 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7526 (pp) outliers start: 189 outliers final: 135 residues processed: 348 average time/residue: 0.1344 time to fit residues: 79.6996 Evaluate side-chains 323 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 168 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 952 ASN Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1060 THR Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 17 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 200 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 307 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097646 restraints weight = 40203.727| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.97 r_work: 0.2955 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26883 Z= 0.130 Angle : 0.657 10.279 36714 Z= 0.309 Chirality : 0.047 0.355 4347 Planarity : 0.004 0.037 4614 Dihedral : 9.141 56.402 5388 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.52 % Allowed : 21.61 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.15), residues: 3174 helix: 0.87 (0.20), residues: 729 sheet: 0.35 (0.20), residues: 705 loop : -1.82 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 396 TYR 0.019 0.001 TYR B1050 PHE 0.015 0.001 PHE B 630 TRP 0.011 0.001 TRP A 869 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00302 (26754) covalent geometry : angle 0.59566 (36369) SS BOND : bond 0.00432 ( 42) SS BOND : angle 1.24568 ( 84) hydrogen bonds : bond 0.04267 ( 899) hydrogen bonds : angle 4.76953 ( 2508) link_ALPHA1-3 : bond 0.00761 ( 3) link_ALPHA1-3 : angle 1.87929 ( 9) link_BETA1-4 : bond 0.01226 ( 33) link_BETA1-4 : angle 3.26591 ( 99) link_NAG-ASN : bond 0.00606 ( 51) link_NAG-ASN : angle 3.36585 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 177 time to evaluate : 1.038 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 25 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6122 (p0) REVERT: A 94 GLU cc_start: 0.7602 (pt0) cc_final: 0.6736 (pt0) REVERT: A 136 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8315 (t0) REVERT: A 413 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 519 ASP cc_start: 0.8521 (t0) cc_final: 0.8143 (t0) REVERT: A 793 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7723 (pp) REVERT: B 94 GLU cc_start: 0.7219 (pt0) cc_final: 0.6984 (pt0) REVERT: B 136 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8300 (t0) REVERT: B 138 PHE cc_start: 0.8495 (m-80) cc_final: 0.8025 (m-10) REVERT: B 152 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: B 265 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9110 (mt) REVERT: B 464 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8467 (p0) REVERT: B 519 ASP cc_start: 0.8526 (t0) cc_final: 0.8203 (t0) REVERT: B 793 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7648 (pp) REVERT: B 933 ASP cc_start: 0.8942 (m-30) cc_final: 0.8706 (t0) REVERT: C 23 PHE cc_start: 0.6374 (OUTLIER) cc_final: 0.5820 (m-10) REVERT: C 25 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6869 (p0) REVERT: C 136 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8454 (t0) REVERT: C 232 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8592 (p90) REVERT: C 413 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8882 (mt) REVERT: C 464 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8513 (p0) REVERT: C 519 ASP cc_start: 0.8617 (t0) cc_final: 0.8228 (t0) REVERT: C 869 TRP cc_start: 0.6575 (p90) cc_final: 0.5981 (p-90) REVERT: C 926 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7953 (p) outliers start: 153 outliers final: 119 residues processed: 315 average time/residue: 0.1554 time to fit residues: 82.6123 Evaluate side-chains 309 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 174 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1119 THR Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 745 GLN Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1060 THR Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 55 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 224 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.097020 restraints weight = 40549.375| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.87 r_work: 0.2946 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26883 Z= 0.180 Angle : 0.679 10.738 36714 Z= 0.321 Chirality : 0.048 0.359 4347 Planarity : 0.004 0.038 4614 Dihedral : 9.080 59.641 5384 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.88 % Allowed : 21.50 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.15), residues: 3174 helix: 0.86 (0.20), residues: 729 sheet: 0.34 (0.19), residues: 720 loop : -1.83 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 748 TYR 0.020 0.001 TYR A1050 PHE 0.015 0.001 PHE A 800 TRP 0.010 0.001 TRP A 424 HIS 0.005 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00437 (26754) covalent geometry : angle 0.61899 (36369) SS BOND : bond 0.00463 ( 42) SS BOND : angle 1.40875 ( 84) hydrogen bonds : bond 0.04547 ( 899) hydrogen bonds : angle 4.78479 ( 2508) link_ALPHA1-3 : bond 0.00599 ( 3) link_ALPHA1-3 : angle 1.89377 ( 9) link_BETA1-4 : bond 0.01191 ( 33) link_BETA1-4 : angle 3.27579 ( 99) link_NAG-ASN : bond 0.00561 ( 51) link_NAG-ASN : angle 3.35262 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 174 time to evaluate : 0.899 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 25 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6016 (p0) REVERT: A 94 GLU cc_start: 0.7710 (pt0) cc_final: 0.6770 (pt0) REVERT: A 136 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8295 (t0) REVERT: A 413 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8763 (mp) REVERT: A 415 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8795 (t0) REVERT: A 519 ASP cc_start: 0.8662 (t0) cc_final: 0.8275 (t0) REVERT: A 600 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: A 793 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7934 (pp) REVERT: B 94 GLU cc_start: 0.7479 (pt0) cc_final: 0.7225 (pt0) REVERT: B 136 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8324 (t0) REVERT: B 138 PHE cc_start: 0.8502 (m-80) cc_final: 0.8014 (m-10) REVERT: B 152 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7499 (m-10) REVERT: B 201 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.8734 (t80) REVERT: B 265 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9164 (mt) REVERT: B 415 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8782 (t0) REVERT: B 464 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8513 (p0) REVERT: B 519 ASP cc_start: 0.8669 (t0) cc_final: 0.8327 (t0) REVERT: B 731 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8462 (tp30) REVERT: B 793 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7704 (pp) REVERT: B 933 ASP cc_start: 0.9150 (m-30) cc_final: 0.8921 (t0) REVERT: C 23 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.5925 (m-10) REVERT: C 25 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6879 (p0) REVERT: C 136 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8414 (t0) REVERT: C 232 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8693 (p90) REVERT: C 413 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8895 (mt) REVERT: C 464 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8560 (p0) REVERT: C 793 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7517 (pp) REVERT: C 869 TRP cc_start: 0.6594 (p90) cc_final: 0.5983 (p-90) REVERT: C 926 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8082 (p) outliers start: 163 outliers final: 129 residues processed: 322 average time/residue: 0.1487 time to fit residues: 81.6823 Evaluate side-chains 320 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 170 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 600 GLN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1119 THR Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 745 GLN Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1060 THR Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 237 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 242 optimal weight: 0.0270 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.095232 restraints weight = 40444.736| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.00 r_work: 0.2915 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26883 Z= 0.211 Angle : 0.709 11.891 36714 Z= 0.338 Chirality : 0.049 0.359 4347 Planarity : 0.004 0.041 4614 Dihedral : 9.091 59.375 5384 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.81 % Allowed : 21.68 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.15), residues: 3174 helix: 0.82 (0.20), residues: 723 sheet: 0.32 (0.19), residues: 717 loop : -1.86 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.020 0.001 TYR A1050 PHE 0.014 0.001 PHE A 630 TRP 0.011 0.001 TRP A 424 HIS 0.006 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00515 (26754) covalent geometry : angle 0.64993 (36369) SS BOND : bond 0.00476 ( 42) SS BOND : angle 1.61219 ( 84) hydrogen bonds : bond 0.04904 ( 899) hydrogen bonds : angle 4.87635 ( 2508) link_ALPHA1-3 : bond 0.00473 ( 3) link_ALPHA1-3 : angle 1.96183 ( 9) link_BETA1-4 : bond 0.01188 ( 33) link_BETA1-4 : angle 3.32924 ( 99) link_NAG-ASN : bond 0.00542 ( 51) link_NAG-ASN : angle 3.38083 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 172 time to evaluate : 0.894 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 25 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6060 (p0) REVERT: A 94 GLU cc_start: 0.7591 (pt0) cc_final: 0.6850 (pt0) REVERT: A 136 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8429 (t0) REVERT: A 413 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8774 (mp) REVERT: A 415 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8692 (t0) REVERT: A 519 ASP cc_start: 0.8533 (t0) cc_final: 0.8158 (t0) REVERT: B 94 GLU cc_start: 0.7403 (pt0) cc_final: 0.7164 (pt0) REVERT: B 136 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8329 (t0) REVERT: B 138 PHE cc_start: 0.8520 (m-80) cc_final: 0.7864 (m-10) REVERT: B 152 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: B 201 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8767 (t80) REVERT: B 265 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9144 (mt) REVERT: B 415 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8646 (t0) REVERT: B 464 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8539 (p0) REVERT: B 517 SER cc_start: 0.9253 (OUTLIER) cc_final: 0.8818 (p) REVERT: B 519 ASP cc_start: 0.8525 (t0) cc_final: 0.8181 (t0) REVERT: B 793 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7719 (pp) REVERT: C 23 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.5871 (m-10) REVERT: C 25 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6939 (p0) REVERT: C 136 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8444 (t0) REVERT: C 232 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8565 (p90) REVERT: C 413 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8900 (mt) REVERT: C 464 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8568 (p0) REVERT: C 731 GLU cc_start: 0.8744 (tp30) cc_final: 0.8336 (tm-30) REVERT: C 793 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7493 (pp) REVERT: C 926 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.7968 (p) outliers start: 161 outliers final: 128 residues processed: 319 average time/residue: 0.1419 time to fit residues: 76.6446 Evaluate side-chains 315 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 167 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 952 ASN Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1119 THR Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1060 THR Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 14 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 305 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 chunk 212 optimal weight: 10.0000 chunk 203 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 259 optimal weight: 0.5980 chunk 173 optimal weight: 0.6980 chunk 217 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 938 ASN ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.097206 restraints weight = 39903.441| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.90 r_work: 0.2955 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26883 Z= 0.134 Angle : 0.659 9.717 36714 Z= 0.312 Chirality : 0.047 0.357 4347 Planarity : 0.004 0.041 4614 Dihedral : 8.855 57.674 5380 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.34 % Allowed : 22.08 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.15), residues: 3174 helix: 0.92 (0.20), residues: 729 sheet: 0.36 (0.19), residues: 717 loop : -1.82 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1002 TYR 0.019 0.001 TYR A1050 PHE 0.019 0.001 PHE A 800 TRP 0.010 0.001 TRP A 869 HIS 0.005 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00318 (26754) covalent geometry : angle 0.59812 (36369) SS BOND : bond 0.00446 ( 42) SS BOND : angle 1.20955 ( 84) hydrogen bonds : bond 0.04230 ( 899) hydrogen bonds : angle 4.71932 ( 2508) link_ALPHA1-3 : bond 0.00535 ( 3) link_ALPHA1-3 : angle 1.89993 ( 9) link_BETA1-4 : bond 0.01225 ( 33) link_BETA1-4 : angle 3.28570 ( 99) link_NAG-ASN : bond 0.00602 ( 51) link_NAG-ASN : angle 3.34255 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 178 time to evaluate : 0.967 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 25 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6135 (p0) REVERT: A 94 GLU cc_start: 0.7535 (pt0) cc_final: 0.6793 (pt0) REVERT: A 136 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8335 (t0) REVERT: A 201 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.8988 (t80) REVERT: A 413 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 519 ASP cc_start: 0.8508 (t0) cc_final: 0.8133 (t0) REVERT: A 793 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7874 (pp) REVERT: B 136 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8321 (t0) REVERT: B 138 PHE cc_start: 0.8473 (m-80) cc_final: 0.7991 (m-10) REVERT: B 152 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7523 (m-10) REVERT: B 201 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8752 (t80) REVERT: B 265 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9134 (mt) REVERT: B 415 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8630 (t0) REVERT: B 464 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8545 (p0) REVERT: B 519 ASP cc_start: 0.8519 (t0) cc_final: 0.8170 (t0) REVERT: B 793 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7724 (pp) REVERT: C 23 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5791 (m-10) REVERT: C 25 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7053 (p0) REVERT: C 136 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8485 (t0) REVERT: C 232 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8600 (p90) REVERT: C 405 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8661 (p) REVERT: C 464 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8526 (p0) REVERT: C 710 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8662 (mtp) REVERT: C 731 GLU cc_start: 0.8663 (tp30) cc_final: 0.8296 (tm-30) REVERT: C 793 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7523 (pp) REVERT: C 869 TRP cc_start: 0.6505 (p90) cc_final: 0.5914 (p-90) REVERT: C 926 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7945 (p) outliers start: 148 outliers final: 122 residues processed: 308 average time/residue: 0.1309 time to fit residues: 68.0809 Evaluate side-chains 314 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 171 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 952 ASN Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1119 THR Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1060 THR Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 91 optimal weight: 0.7980 chunk 205 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 223 optimal weight: 0.3980 chunk 212 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 214 optimal weight: 0.3980 chunk 286 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 315 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099948 restraints weight = 40153.263| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.84 r_work: 0.3006 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26883 Z= 0.115 Angle : 0.628 9.504 36714 Z= 0.297 Chirality : 0.046 0.357 4347 Planarity : 0.004 0.038 4614 Dihedral : 8.398 57.437 5374 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.91 % Allowed : 22.47 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.15), residues: 3174 helix: 1.16 (0.21), residues: 720 sheet: 0.54 (0.20), residues: 705 loop : -1.77 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1002 TYR 0.019 0.001 TYR A1050 PHE 0.020 0.001 PHE A 630 TRP 0.009 0.001 TRP A 246 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00268 (26754) covalent geometry : angle 0.56792 (36369) SS BOND : bond 0.00434 ( 42) SS BOND : angle 0.98417 ( 84) hydrogen bonds : bond 0.03658 ( 899) hydrogen bonds : angle 4.54720 ( 2508) link_ALPHA1-3 : bond 0.00575 ( 3) link_ALPHA1-3 : angle 1.86737 ( 9) link_BETA1-4 : bond 0.01215 ( 33) link_BETA1-4 : angle 3.21308 ( 99) link_NAG-ASN : bond 0.00589 ( 51) link_NAG-ASN : angle 3.25250 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4961.87 seconds wall clock time: 86 minutes 20.21 seconds (5180.21 seconds total)